A. F. , Essai des eaux. Détermination de l' Indice Biologique Global Normalisé (IBGN), pp.90-350, 1992.

A. F. , Détermination de l'indice biologique macrophytique en rivière (IBMR), vol.AFNOR, 2003.

A. Baattrup-pedersen and T. Riis, Macrophyte diversity and composition in relation to substratum characteristics in regulated and unregulated Danish streams, Freshwater Biology, vol.42, pp.375-385, 1999.

F. Bensettiti, V. Gaudillat, and J. Haury, Cahier d'Habitats Natura2000. Habitats humides. Connaissances et gestion des habitats et des espèces d'intérêts communautaire, 2002.

A. Compin and R. Céréghino, Sensitivity of aquatic insect species richness to disturbance in the AdourGaronne stream system (France), Ecological Indicators, vol.3, pp.135-142, 2003.

J. A. Cotton, G. Wharton, J. A. Bass, C. M. Heppell, and R. S. Wotton, The effects of seasonal changes to in-stream vegetation cover on patterns of flow and accumulation of sediment, Geomorphology, vol.77, pp.320-334, 2006.

E. Union, Directive 92/43/EEC of the Council of 21 May 1992 on the Conservation of Natural Habitats and of Wild Fauna and Flora. European Centre for Nature Conservation, 1992.

J. Haury, M. C. Peltre, M. Trémolières, J. Barbe, G. Thiébaut et al., A new method to assess water trophy and organic pollution -the Macrophyte Biological Index for Rivers (IBMR): its application to different types of river and pollution, Hydrobiologia, vol.570, pp.153-158, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01453662

D. Hering, C. Meier, C. Rawer-jost, C. K. Feld, R. Biss et al., Assessing streams in Germany with benthic invertebrates: selection of candidate metrics, Limnologica, vol.34, pp.398-415, 2004.

R. K. Johnson, D. Hering, M. T. Furse, and R. T. Clarke, Detection of ecological change using multiple organism groups: metrics and uncertainty, Hydrobiologia, vol.566, pp.115-137, 2006.

R. Julliard, J. Clavel, V. Devictor, F. Jiguet, and D. Couvet, Spatial segregation of specialists and generalists in bird communities, Ecology Letters, vol.9, pp.1237-1244, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00113560

R. Julliard and F. Jiguet, Un suivi intégré des populations d' oiseaux communs en France, Alauda, vol.70, pp.137-147, 2002.

D. R. Lenat, Water quality assessment of streams using a qualitative collection method for benthic macroinvertebrates, Journal of the North American Benthological Society, vol.7, pp.222-233, 1988.

R. H. Norris and A. Georges, Analysis and interpretation of benthic surveys, Freshwater Biomonitoring and Benthic Macroinvertebrates, pp.234-286, 1993.

J. L. Read, N. Reid, and W. N. Venables, Which Birds Are Useful Bioindicators of Mining and Grazing Impacts in Arid South Australia?, Environmental Management, vol.26, pp.215-232, 2000.

V. H. Resh and J. K. Jackson, Rapid assessment approaches to biomonitoring using benthic macroinvertebrates, Freshwater Biomonitoring and Benthic Macroinvertebrates, pp.195-223, 1993.

L. Sandin and L. B. Johnson, Statistical power of selected indicator metrics using macroinvertebrates for assessing acidification and eutrophication of running waters, Hydrobiologia, vol.422, pp.171-179, 2000.

A. Baattrup-pedersen and T. Riis, Macrophyte diversity and composition in relation to substratum characteristics in regulated and unregulated Danish streams, Freshwater Biology, vol.42, pp.375-385, 1999.

P. Bourrelly, Les algues d'eau douce. N. Boubée & Cie, 1966.

J. Bravard, C. Amoros, G. Pautou, G. Bornette, M. Bournaud et al., River incision in south-east France: morphological phenomena and ecological effects, vol.13, pp.75-90, 1997.

A. Brookes, Stream Ecology: Structure and Function of Running Waters, 1985.

J. N. Beisel, P. Usseglio-polatera, S. Thomas, and J. C. Moreteau, Effects of mesohabitat sampling strategy on the assessment of stream quality with benthic invertebrate assemblages, Archiv für Hydrobiologie, vol.142, pp.493-510, 1998.

F. Bensettiti, V. Gaudillat, and J. Haury, Cahier d'Habitats Natura2000. Habitats humides. Connaissances et gestion des habitats et des espèces d'intérêts communautaire, 2002.

P. J. Boon, Essential elements in the case for river conservation, River Conservation and Management, pp.11-33, 1992.

G. Bornette and C. Amoros, Aquatic vegetation and hydrology of a braided river floodplain, Journal of Vegetation Science, vol.2, pp.497-512, 1991.

G. Bornette, C. P. Henry, M. H. Barrat, and C. Amoros, Theoretical habitat templets, species traits and species richness: aquatic macrophytes in the Upper Rhône River and its floodplain, Freshwater Biology, vol.31, pp.487-505, 1994.

P. Bourrelly, Les algues d'eau douce. N. Boubée & Cie, 1966.

M. M. Brinson, B. L. Swift, R. C. Plantico, and J. S. Barclay, Riparian ecosystems: their ecology and status, 1981.

S. S. Brooks, M. A. Palmer, B. J. Cardinale, C. M. Swan, and S. Ribblett, Assesing stream ecosystem rehabilitation: limitations of community structure data, Restoration Ecology, vol.10, pp.156-168, 2002.

B. L. Brown, Spatial heterogeneity reduces temporal variability in stream insect communities, Ecology Letters, vol.6, pp.316-325, 2003.

R. Carbiener, M. Trémolières, J. L. Mercier, and A. Ortscheit, , 1990.

D. Chessel, A. Dufour, and J. Thioulouse, The ade4 package-I-One-table methods, R News, vol.4, pp.5-10, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00427558

F. Chevenet, S. Dolédec, and D. Chessel, A fuzzy coding approach for the analysis of long-term ecological data, Freshwater Biology, vol.31, pp.295-309, 1994.

I. Combroux, G. Bornette, N. J. Willby, and C. Amoros, Regenerative strategies of aquatic plants in disturbed habitats: the role of propagule banks, Archiv für Hydrobiologie, vol.152, pp.215-235, 2001.

J. H. Connell and R. O. Slatyer, Mechanisms of succession in natural communities and their role in community stability and organisation, American Naturalist, vol.111, pp.1119-1144, 1977.

R. Corillion, Flore de Charophytes (Characées) du Massif Armoricain et des contrées voisines d' Europe occidentale. In: Jouve Editeurs, pp.11-216, 1975.

K. P. Brodersen, 100 years of vegetation decline and recovery in Lake Fure, Denmark. Journal of Ecology, vol.96, pp.260-271, 2008.

M. Schulz and B. Gücker, Macrophytes Increase Spatial Patchiness of Fluvial Sedimentary Records and Effect Temporal Particulate Nutrient Storage, Aquatic Geochemistry, vol.11, pp.89-107, 2005.

A. J. Smith, The Moss Flora of Britain and Ireland, Cambridge. Smith A.J.E, 1978.

T. R. Southwood, Habitat: the templet for ecological strategies, Journal of Animal Ecology, vol.46, pp.337-365, 1977.

T. R. Southwood, Tactics, strategies and templets, vol.52, pp.3-18, 1988.

H. M. Stevens and W. P. Carson, Resource quantity, not resource heterogeneity maintains plant diversity, Ecological Letters, vol.5, pp.420-426, 2002.

J. Szmeja and E. Bazydlo, The effect of water conditions on the phenology and age structure of Luronium natans (L.) raf. populations Acta Societatis Botanicorum Polonia, vol.74, pp.253-262, 2005.

S. Tomanova and P. Usseglio-polatera, Patterns of benthic community traits in neotropical streams: relationship to mesoscale spatial variability, Fundamental and Applied Limnology, vol.170, pp.243-255, 2007.

C. R. Townsend and A. G. Hildrew, Species traits in relation to a habitat templet for river systems, Freshwater Biology, vol.31, pp.265-276, 1994.

T. G. Tutin, V. H. Heywood, N. A. Burges, D. M. Moore, D. H. Valentine et al., Flora Europea, 1964.

J. G. Wasson, J. R. Malavoi, L. Maridet, Y. Souchon, and L. Paulin, Impacts écologiques de la chenalisation des rivières. Cemagref éditions, coll. Etudes, série Gestion des Milieux Aquatiques, 1995.

N. J. Willby, V. J. Abernethy, and B. O. Demars, Attribute-based classification of European hydrophytes and its relationship to habitat utilization, Freshwater Biology, vol.43, pp.43-74, 2000.

A. F. , Essai des eaux. Détermination de l' Indice Biologique Global Normalisé (IBGN), pp.90-350, 1992.

A. F. , Qualité de l' eau. Détermination de l' indice biologique diatomées (IBD), 2000.

, Association Française de Normalisation -norme homologuée T, pp.90-354

A. F. , Détermination de l'indice biologique macrophytique en rivière (IBMR), 2003.

P. Acot, Histoire de l' écologie, 1988.

A. De and L. Eau, Système d' Evaluation de la Qualité du milieu physique des cours d' eau, SEQ Physique -Version 1. Rapport de présentation, p.32, 1998.

A. De and L. Eau, Système d' Evaluation de la Qualité biologique des cours d' eau, SEQ Biologie -Version 0 -Principes généraux, p.27, 2000.

A. De and L. Eau, Système d' Evaluation de la Qualité de l' eau des cours d' eau, SEQ eau -Version 1 -Principes généraux. Etude interagences, n°64, p.21, 2000.

A. De and L. '-eau-seine-normandie, La Qualité des cours d' eau du Bassin Seine Amont, pp.1-12, 1995.

. Agence-européenne-de-l'environnement, L'Environnement à l'aube du XXIème siècle, 1999.

. Agence-européenne-de-l'environnement, L'Environnement en Europe, troisième évaluation (Résumé), 2003.

A. De and L. Eau, Etude des Agences de l' eau n°00. Indice Biologique Global Normalisé I.B.G.N, NF -T 90 -350. Guide technique, pp.1-21, 2000.

J. D. Allan, Stream Ecology: Structure and Function of Running Waters, 1995.

J. D. Allan and A. S. Flecker, Biodiversity conservation in running waters, Bioscience, vol.43, pp.32-43, 1993.

P. Allee, G. Giert, and R. Mussot, Aménagement des rivières à fond mobile: évolution des sections fluviales aménagées, p.86, 1981.

C. Amoros, A. L. Roux, and J. L. Reygrobellet, A method for applied ecological studies of fluvial hydrosystems, Regulated Rivers: Research and Management, vol.1, pp.17-36, 1987.

P. L. Angermeier, R. A. Smogor, and J. R. Stauffer, Regional frameworks and candidate metrics for assessing biotic integrity in mid-Atlantic highland streams, Transactions of the American Fisheries Society, vol.129, pp.962-981, 2000.

. Bibliographie,

. Anonyme, Système d' évaluation de la qualité des cours d' eau, Les études des agences de l' eau. -Agences de l' eau, p.59, 1999.

V. Archaimbault, Réponses bio-écologiques des macroinvertébrés benthiques aux perturbations : la base d'un outil diagnostique fonctionnel des écosystèmes d, 2003.

A. H. Arthington and R. L. Welcomme, The condition of large river systems of the World, Condition of the World's Aquatic Habitats. -World Fisheries Congress, pp.44-75, 1995.

A. Baattrup-pedersen, S. E. Larsen, and T. Riis, Long-term effects of stream management on plant communities in two Danish lowland streams, Hydrobiologia, vol.481, pp.33-45, 2002.

A. Baattrup-pedersen, S. E. Larsen, and T. Riis, Composition and richness of macrophyte communities in small Danish streams -influence of environmental factors and weed cutting, Hydrobiologia, vol.495, pp.171-179, 2003.

A. Baattrup-pedersen and T. Riis, Macrophyte diversity and composition in relation to substratum characteristics in regulated and unregulated Danish streams, Freshwater Biology, vol.42, pp.375-385, 1999.

P. Bady, S. Dolédec, C. Fesl, S. Gayraud, M. Bacchi et al., Use of invertebrate traits for the biomonitoring of European large rivers: the effects of sampling effort on genus richness and functional diversity, Freshwater Biology, vol.50, pp.159-173, 2005.
URL : https://hal.archives-ouvertes.fr/halsde-00340560

M. B. Bain, J. T. Finn, and H. E. Booke, Streamflow regulation and fish community structure, Ecology, vol.69, pp.382-392, 1988.

R. Barbault, Biodiversité -introduction à la biologie de la conservation, 1997.

R. Barbault, Ecologie Générale. Structure et Fonctionnement de la Biosphère. 6 ème édition, 2008.

M. T. Barbour, J. Gerritsen, B. D. Snyder, and J. B. Stribling, Rapid bioassessment protocols for use in streams and wadeable rivers: periphyton, benthic macroinvertebrates and fish, 1998.

M. T. Barbour, J. Gerritsen, B. D. Snyder, and J. B. Stribling, Rapid Bioassessment Protocols for Use in Streams and Rivers: Periphyton, Benthic Macroinvertebrates, and Fish, 1999.

P. A. Bisson, K. Sullivan, and J. L. Nielsen, Channel hydraulics, habitat use and body form of juvenile coho salmon, steelhead, and cutthroat trout in streams, Transactions of the American Fisheries Society, vol.117, pp.262-273, 1988.

J. Blondel, L' analyse des peuplements d' oiseaux, Eléments d' un diagnostic écologique: I. La Méthode des Echantillons Fréquentiels Progressifs (EFP). Revue d' Ecologie Appliquée (Terre et Vie), vol.29, pp.533-589, 1975.

J. Blondel, « De la théorie au concret : la biologie de la conservation ». NatureSciences-Société Hors série, pp.10-18, 1995.

J. Blondel, Allocution de clôture, Premières journées francophones de biologie de la conservation, 2003.

P. J. Boon, Essential elements in the case for river conservation, River Conservation and Management, pp.11-33, 1992.

G. Bornette and C. Amoros, Disturbance regimes and vegetation dynamics: role of floods in riverine wetlands, Journal of Vegetation Sciences, vol.7, pp.615-622, 1996.

G. Bornette, C. Amoros, and D. Chessel, Effect of allogenic processes on successional rates in former river channels, Journal of Vegetation Science, vol.5, pp.237-246, 1994.

V. Boullet, Notion d' Habitat d' Espèce Végétale. Fédération des Conservatoires Botaniques Nationaux, 2002.

P. Bourrelly, Les algues d'eau douce. N. Boubée & Cie, 1966.

K. D. Bovee, A guide to stream habitat analysis using the Instream Flow Incremental Methodology, Flow Information Paper, 1982.

J. Bravard, C. Amoros, G. Pautou, G. Bornette, M. Bournaud et al., River incision in south-east France: morphological phenomena and ecological effects, vol.13, pp.75-90, 1997.

P. A. Brewin, S. T. Buckton, and S. J. Ormerod, River habitat surveys and biodiversity in acid-sensitive rivers. Aquatic Conservation -Marine and Freshwater Ecosystems, vol.8, pp.501-514, 1998.

G. J. Brierley, Channel morphology and element assemblages: a constructivist approach to facies modelling, Advances in Fluvial Dynamics and Stratigraphy, pp.263-298, 1996.

A. Brookes, River channelization: traditional engineering methods, physical consequences and alternative practices, Progress in Physical Geography, vol.9, pp.44-73, 1985.

A. Brookes, Channelized rivers. Perspectives for environmental management, 1988.

J. H. Brown and M. V. Lomolino, Biogeography. Sinauer, 1998.

S. A. Bryce, R. M. Hughes, and P. R. Kaufmann, Development of a bird integrity index : Using Bird assembly as Indicators of riparian condition, Environmental Management, vol.30, pp.294-310, 2002.

S. T. Buckton and S. J. Ormerod, Use of a new standardized habitat survey for assessing the habitat preferences and distribution of upland river birds, Bird Study, vol.44, pp.327-337, 1997.

S. E. Bunn and P. M. Davies, Biological processes in running waters and their implications for the assessment of ecological integrity, Hydrobiologia, vol.422, pp.61-70, 2000.

R. W. Butcher, Studies on the ecology of rivers. 1. On the distribution of macrophyte vegetation in the rivers of Britain, Journal of Ecology, vol.21, pp.58-91, 1933.

J. Cacas, M. Degoutte, A. Dutartre, F. Gross, and M. Vuillot, Aménagements de rivières: trois études de cas. Cemagref (Ministère de l' Environnement, 1986.

J. Cairns, Ecological integrity of aquatic systems, Regulated Rivers: Research and Management, vol.11, pp.313-324, 1995.

J. Cairns and J. R. Pratt, On the relation between structural and functional analyses of ecosystems, Environmental Toxicology and Chemistry, vol.5, pp.785-786, 1986.

P. Calow and G. E. Petts, The Rivers Handbook Blackwell Scientific, 1994.

N. F. Caraco, Disturbance of the phosphorus cycle: A case of indirect effects of human activity, Tree, vol.8, issue.2, 1993.

R. Carbiener, M. Trémolières, J. L. Mercier, and A. Ortscheit, Aquatic macrophyte communities as bioindicators of eutrophication in calcareous oligosaprobe stream waters Upper Rhine plain, Alsace. Vegetatio, vol.86, pp.71-88, 1990.

C. Grenoble, L' étude d, 1983.

P. D. Champion and C. C. Tanner, Seasonality of macrophytes and interaction with flow in a New Zealand lowland stream, Hydrobiologia, vol.441, pp.1-12, 2000.

. Bibliographie,

F. S. Chapin, E. S. Zavelata, V. T. Eviner, R. L. Naylor, P. M. Vitousek et al., Consequences of changing biodiversity, Nature, vol.405, pp.234-242, 2000.

M. Cheylan, Evaluation patrimoniale des espèces et des espaces : quels critères adopter ? EPHE, Module d' enseignement "Biologie de la conservation, 2000.

F. E. Clements, Research Methods in Ecology, 1905.

I. Combroux, J. Servan, and J. Moret, Méthodes utilisées dans le suivi d'habitats et d'espèces de faune et de flore -Synthèse bibliographique, Muséum National d' Histoire Naturelle, p.158, 2004.

, Cinquième programme communautaire de politique et d' action pour l' environnement et le développement durable et respectueux de l' environnement intitulé "Vers un développement soutenable" -COM92, 1992.

A. Compin and R. Céréghino, Sensitivity of aquatic insect species richness to disturbance in the Adour-Garonne stream system (France), Ecological Indicators, vol.3, pp.135-142, 2003.

J. Connell, Diversity in tropical rain forests and coral reefs, Science, pp.1302-1310, 1978.

, Convention on Biological Diversity. Article 2, Convention on Biological Diversity, 1992.

S. E. Cook, Quest for an index of community structure sensitive to water pollution, Environmental Pollution, vol.11, pp.269-288, 1976.

S. D. Cooper, S. Diehl, K. Kratz, and O. Sarnelle, Implications of scale for patterns and processes in stream ecology, Australian Journal of Ecology, vol.23, pp.27-40, 1998.

H. Coops, F. W. Van-den-brink, and G. Van-der-velde, Growth and morphological responses of four helophyte species in an experimental water-depth gradient, Aquatic Botany, vol.54, pp.11-24, 1996.

, Decisions Adopted by the Conference of the Parties to the Convention on Biological Diversity at its Seventh Meeting, p.7, 2004.

E. Coring, Situation and developments of algal (diatom)-based techniques for monitoring rivers in Germany, Use of Algae for Monitoring Rivers III. -Agence de l'Eau, pp.122-127, 1999.

. Bibliographie,

R. Costanza, Toward an operational definition of ecosystem health, Ecosystem Health: New Goals for Environmental Management, pp.239-256, 1992.

R. Costanza, R. De-groot, R. Farberk, S. Grasso, M. Hannon et al., The value of the world's ecosystem services and natural capital, Nature, vol.387, pp.253-260, 1997.

J. Coudreuse, J. Haury, J. Bardat, and J. P. Rebillard, Les bryophytes aquatiques et supraaquatiques : clé d'identification pour la mise en oeuvre de l'Indice Biologique Macrophytiques en Rivière, 2005.

D. A. Crook, A. I. Robertson, A. J. King, and &. Humphries, The influence of spatial scale and habitat arrangement on diel patterns of habitat use by two lowland river fishes, Oecologia, vol.129, pp.525-533, 2001.

M. J. Croonquist and R. P. Brooks, Use of avian and mammalian guilds as indicators of cumulative impacts in riparian wetland areas, Environmental Management, vol.15, pp.701-714, 1991.

R. Cuinat, Vers un aménagement plus raisonnable des berges et du lit de nos cours d' eau, vol.48, p.3, 1979.

G. C. Daily, Nature's Services: Societal Dependence on Natural Ecosystems, 1997.

H. Daniel, Evaluation de la qualité des cours d' eau par la végétation macrophytique. Travail in situ et expérimental dans le Massif armoricain sur les pollutions par les macronutriments, 1998.

F. H. Dawson, Water flow and the vegetation of running waters, Vegetation of Inland Waters, pp.283-309, 1988.

N. De-pauw and G. Vanhooren, Methods for biological assessment for water courses in Belgium, Hydrobiologia, vol.100, pp.153-168, 1983.

M. D. Dettinger and H. F. Diaz, Global characteristics of stream flow seasonality and variability, Journal of Hydrometeorology, vol.1, pp.289-310, 2000.

V. Devictor, R. Julliard, J. Clavel, F. Jiguet, A. Lee et al., Functional biotic homogenization of bird communities in disturbed landscapes, Global ecology and biogeography letters, vol.17, pp.252-261, 2008.

S. Diaz and M. Cabido, Vive la différence: plant functional diversity matters to ecosystem processes, TRENDS in Ecology and Evolution, vol.16, pp.646-655, 2001.

B. Fox and J. F. , Intermediate-disturbance hypothesis, Science, vol.204, pp.1344-1345, 1979.

J. F. Franklin, Preserving Biodiversity: Species, Ecosystems, or Landscapes?, Ecological Applications, vol.3, pp.202-205, 1993.

C. A. Frissell, W. J. Liss, C. E. Warren, and M. D. Hurley, A hierarchical framework for stream habitat classification: viewing streams in a watershed context, Environmental Management, vol.10, pp.199-214, 1986.

B. Frochot, B. Faivre, V. Godreau, and J. Roché, Les forêts riveraines des cours d'eau, Ecologie, fonctions et gestion. -IDF, pp.156-168, 2003.

P. S. Giller and B. Malmqvist, The Biology of Streams and Rivers, 1998.

A. Giorgi, C. Feijoo, and G. Tell, Primary producers in a Pampean stream: temporal variation and structuring role, Biodiversity and Conservation, vol.14, pp.1699-1718, 2005.

P. H. Gleick, Water resources, Encyclopedia of Climate and Weather, pp.817-823, 1996.

G. Glova and M. J. Duncan, Potential effects of reduced flows on fish habitats in a large braided river, Transactions of the American Fisheries Society, vol.114, pp.165-181, 1985.

V. Godreau, G. Bornette, B. Frochot, C. Amoros, E. Castella et al., Biodiversity in the floodplain of Saône : A global approach, Biodiversity and Conservation, vol.8, pp.839-864, 1999.

N. M. Gomez, The Pampean Diatom Index (IDP) for assessment of rivers and streams in Argentina, Aquatic Ecology, vol.35, pp.173-181, 2001.

N. Grasmück, La végétation aquatique des cours d' eau de Lorraine: typologie floristique et écologique. Contribution à l' étude de l' autoécologie des espèces de la flore aquatique lorraine, 1994.

J. S. Gray, K. R. Clarke, R. M. Warwick, and G. Hobbs, Detection of initial effects of pollution on marine benthos: an example from the Ekofisk and Eldfisk oilfields, Marine Ecology Progress Series, vol.66, pp.285-299, 1990.

J. S. Gray and K. Jensen, Feedback monitoring: a new way of protecting the environment, TRENDS in Ecology and Evolution, vol.8, pp.267-268, 1993.

W. W. Gregg and F. L. Rose, Influences of aquatic macrophytes on invertebrate community structure, guild structure, and microdistribution in streams, Hydrobiologia, vol.128, pp.45-56, 1985.

. Bibliographie,

M. B. Griffith, B. H. Hill, F. H. Mccormick, P. R. Kaufmann, A. T. Herlihye et al., Comparative application of indices of biotic integrity based on periphyton, macroinvertebrates, and fish to southern Rocky Mountain streams, Ecological Indicators, vol.5, pp.117-136, 2005.

D. Harper, C. D. Smith, P. Barham, and R. Howell, The ecological basis for the management of the natural river environment, The Ecological Basis for River Management, pp.219-238, 1995.

D. M. Harper, C. D. Smith, and P. J. Barham, Habitats as the building blocks for river conservation assessment, River Conservation and Management, 1992.

J. H. Harris and R. Silveira, Large-scale assessments of river health using an index of biotic integrity with low diversity fish communities, Freshwater Biology, vol.41, pp.235-252, 1999.

S. M. Haslam, River Plants: The macrophytic vegetation of watercourses, 1978.

J. Haury, Assessing functional typology involving water quality, physical features and macrophytes in a Normandy river, Hydrobiologia, vol.340, pp.43-49, 1996.

J. Haury, M. C. Peltre, M. Trémolières, J. Barbe, G. Thiébaut et al., A new method to assess water trophy and organic pollution -the Macrophyte Biological Index for Rivers (IBMR): its application to different types of river and pollution, Hydrobiologia, vol.570, pp.153-158, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01453662

D. J. Hawksworth and M. T. Kalin-arroyo, Magnitude and distribution of biodiversity, Global biodiversity Assessment, pp.107-191, 1995.

A. Henderson, J. Comiskey, F. Dallmeier, and A. Alonso, Framework for Assessment and Monitoring of, Biodiversity. Encyclopedia of biodiversity, pp.1-11, 2001.

C. P. Henry and C. Amoros, Restoration ecology of riverine wetlands: I. A scientific base, Environmental Management, vol.19, pp.891-902, 1995.

D. Hering, O. Moog, L. Sandin, and P. F. Verdonschot, Overview and application of the AQEM assessment system, Hydrobiologia, vol.516, pp.1-20, 2004.

B. H. Hill, A. T. Herlihy, P. R. Kaufmann, J. R. Stevenson, F. H. Mccormick et al., Use of periphyton assemblage data as an index of biotic integrity, Journal of the North American Benthological Society, vol.19, pp.50-67, 2000.

N. T. Holmes, The macrophytic vegetation of the river Tees in 1975: observed and predicted changes, Freshwater Biology, vol.7, pp.43-60, 1977.

N. T. Holmes, Typing British rivers according to their flora. (ed.): Focus on Nature Conservation, 1983.

N. T. Holmes, J. R. Newman, S. Chadd, K. J. Rouen, L. Saint et al., Mean Trophic Rank: A Users Manual, Environment Agency, 1999.

R. M. Hughes, Defining acceptable biological status by comparing with reference conditions, Biological Assessment and Criteria: Tools for Water Resource Planning and Decision Making, pp.31-48, 1995.

G. E. Hutchinson, Homage to Santa Rosalia or why are there so many kinds of animals?, American Naturalist, vol.93, pp.145-159, 1959.

J. Illies and L. Botosaneanu, Problèmes et méthodes de la classification et de la zonation écologique des eaux courantes considerées surtout du point de vue faunistique, Verhandlungen der Internationalen Vereinigung für Theoretische und Angewandte Limnologie, vol.12, pp.1-57, 1963.

, The Durban Accord, 2003.

G. A. Jagers-op-akkerhuis, Analysing hierarchy in the organization of biological and physical systems, Biological Reviews, pp.1-12, 2007.

P. Jepson and S. Canney, Biodiversity hotspots: hot for what? Global ecology and biogeography letters 10, pp.225-227, 2001.

F. Jiguet and R. Julliard, Instruction pour le programme STOC-EPS 2003, 2003.

M. Jonsson and B. Malmqvist, Ecosystem process rate increases with animal species richness: evidence from leaf-eating, aquatic insects, Oikos, vol.89, pp.519-523, 2000.

I. G. Jowett, Instream flow methods: a comparison of approaches, Research and Management, vol.13, pp.115-127, 1997.

R. Julliard, J. Clavel, V. Devictor, F. Jiguet, and D. Couvet, Spatial segregation of specialists and generalists in bird communities, Ecology Letters, vol.9, pp.1237-1244, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00113560

R. Julliard and F. Jiguet, Un suivi intégré des populations d' oiseaux communs en France, Alauda, vol.70, pp.137-147, 2002.

M. Jungwirth, S. Muhar, and S. Schmutz, Re-establishing and assessing ecological integrity in riverine landscapes, Freshwater Biology, vol.47, pp.867-887, 2002.

B. Junk, W. J. Bayley, P. B. Sparks, and R. E. , The flood pulse concept in river-floodplain, 1989.

A. R. Ladson, L. J. White, J. A. Doolan, B. L. Finlayson, B. T. Hart et al., Development and testing of an Index of Stream Condition for waterway management in Australia, Freshwater Biology, vol.41, pp.453-468, 1999.

C. Larrère and R. Larrère, Du bon usage de la nature, pour une philosophie de l'environnement, 1997.

M. Lazaridou-dimitriadou, Seasonal variation of the water quality of rivers and streams of eastern Mediterranean, Web Ecology, vol.3, pp.20-32, 2002.

J. C. Lefeuvre, De la protection de la nature à la gestion du patrimoine naturel, Patrimoines en folie. -Ed. de la Maison des sciences de l'homme, p.297, 1990.

H. V. Leland, Distribution of phytobenthos in the Yakima River basin, Washington, in relation to geology, land use, and other environmental factors, Canadian Journal of Fisheries and Aquatic Sciences, vol.52, pp.1108-1129, 1995.

D. R. Lenat, Water quality assessment of streams using a qualitative collection method for benthic macroinvertebrates, Journal of the North American Benthological Society, vol.7, pp.222-233, 1988.

J. L. Li, A. Herlihy, W. Gerth, P. Kaufmann, S. Gregory et al., Variability in stream macroinvertebrates at multiple spatial scales, Freshwater Biology, vol.46, pp.1-87, 2001.

M. Loreau, Biodiversity and ecosystem functioning: a mechanistic model, Proceedings of the National Academy of Sciences USA, vol.95, pp.5632-5636, 1998.

M. Loreau, S. Naeem, P. Inchausti, J. Bengtsson, J. P. Grime et al., Biodiversity and ecosystem functioning: current knowledge and future challenges, Science, vol.294, pp.804-808, 2001.

V. Lüderitz, R. Jüpner, S. Müller, and C. K. Feld, Renaturalization of streams and riversthe special importance of integrated ecological methods in measurement of success. An example from Saxony-Anhalt (Germany), Limnologica, vol.34, pp.249-263, 2004.

R. L. Mackey and D. J. Currie, A re-examination of the expected effects of disturbance on diversity, Oikos, vol.88, pp.483-493, 2000.

I. Maddock, The importance of physical habitat assessment for evaluating river health, Freshwater Biology, vol.41, pp.373-391, 1999.

B. Malavoi and J. R. , Typologie des faciès d'écoulement ou unités morphodynamiques des cours d'eau à haute énergie, Bulletin Français de Pêche et de Pisciculture, vol.315, pp.189-210, 1989.

J. R. Malavoi, Méthodologie de sectorisation et de description des cours d' eau à pente forte et moyenne: application à une gestion intégrée des écosystèmes d, 1990.

. Thesis and . Type,

J. R. Malavoi and Y. Souchon, Description standardisée des principaux faciès d' écoulement observables en rivière: clé de détermination qualitative et mesures physiques, Bulletin Français de Pêche et de Pisciculture, vol.365, pp.357-372, 2002.

B. Malmqvist and S. Rundle, Threats to the running water ecosystems of the world, Environmental Conservation, vol.29, pp.134-153, 2002.

S. Manel, S. T. Buckton, and S. J. Ormerod, Testing large-scale hypotheses using surveys: the effects of land use on the habitats, invertebrates and birds of Himalayan rivers, Journal of Applied Ecology, vol.37, pp.756-770, 2000.
URL : https://hal.archives-ouvertes.fr/halsde-00295512

L. Maridet, La végétation rivulaire, facteur de contrôle du fonctionnement écologique des cours d' eau : influence sur les communautés benthiques et hyporhéiques et sur les peuplements de poissons dans trois cours d' eau du Massif Central. Thesis. Type, 1996.

C. Mason and S. M. Macdonald, Numbers of wintering waterbirds on rivers in eastern England, Wildfowl, vol.51, pp.215-219, 2000.

C. F. Mason, Biology of freshwater pollution, 1991.

N. W. Mason, K. Macgillivray, J. B. Steel, and J. B. Wilson, An index of functional diversity, Journal of Vegetation Sciences, vol.14, pp.571-578, 2003.

E. Mayr, The growth of biological thought: diversity, evolution, and inheritance, 1982.

G. K. Meffe and C. R. Carroll, Principles of conservation biology -second edition, 1997.

J. L. Metcalfe, Biological water-quality assessment of running waters based on macroinvertebrate communities -history and present status in Europe, Environmental Pollution, vol.60, pp.101-139, 1989.

, Ecosystems and Human Well-being, Biodiversity Synthesis. World Resources Institute, 2005.

D. Mouillot, N. W. Mason, O. Dumay, and J. B. Wilson, Functional regularity: a neglected aspect of functional diversity, Oecologia, vol.142, pp.353-359, 2005.

D. Mueller-dombois and H. Ellenberg, Aims and Methods of Vegetation Ecology, 1974.

. Wiley,

S. Muhar, Habitat improvment of Austrian Rivers with regards to different scales, Regulated Rivers: Research and Management, vol.12, pp.471-482, 1996.

A. Munné, N. Prat, C. Solà, N. Bonada, and M. Rieradevall, A simple method for assessing the ecological quality of riparian habitat in rivers and streams: QBR index. Aquatic Conservation: Marine and Freshwater Ecosystems, vol.13, pp.147-163, 2003.

A. Muratet, E. Porcher, V. Devictor, G. Arnal, J. Moret et al., Evaluation of floristic diversity in urban areas as a basis for habitat management, Applied Vegetation Science, vol.11, pp.451-460, 2008.

N. Myers, The biodiversity challenge: expanded hot-spots analysis, Environmentalist, vol.10, pp.243-256, 1990.

N. Myers, R. A. Mittermeier, C. G. Mittermeier, G. A. Da-fonseca, and J. Kent, , 2000.

, Biodiversity hotspots for conservation priorities, Nature, vol.403, pp.853-858

S. Naeem, F. S. Chapin, R. Costanza, P. R. Ehrlich, F. B. Golley et al., , 1999.

, Biodiversity and ecosystem functioning: maintaining natural life support processes, Issues in Ecology, vol.4, pp.1-13

R. J. Naiman and H. Decamps, The ecology of interfaces-riparian zones, Annual Review of Ecology and Systematics, vol.28, pp.621-658, 1997.

R. J. Naiman, J. J. Magnuson, D. M. Mcknight, and J. A. Stanford, The Freshwater Imperative -A Research Agenda, 1995.

F. K. Nakamura, K. Tockner, and K. Amano, River and wetland restoration: lessons from Japan, Bioscience, vol.56, pp.419-429, 2006.

S. Nakano and M. Murakami, Reciprocal subsidies: Dynamic interdependence between terrestrial and aquatic food webs, Proceedings of the National Academy of Sciences USA, vol.98, pp.166-170, 2001.

J. D. Newbold, J. W. Elwood, R. V. Vanwinkle, and W. , Nutrient spiralling in streams: Implications for nutrient limitation and invertebrate activity, American Naturalist, vol.120, pp.628-652, 1982.

R. W. Newbury and M. N. Gaboury, Stream analysis and fish habitat design. Newbury Hydraulics Ltd, Manitoba Natural Resources, 1993.

C. Nilsson and K. Berggren, Alterations of riparian ecosystems caused by river regulation, Bioscience, vol.50, pp.783-792, 2000.

C. Nilsson, C. A. Reidy, M. Dynesius, and C. Revenga, Fragmentation and flow regulation of the world's large river systems, Science, vol.308, pp.405-408, 2005.

R. H. Norris, Rapid biological assessment, natural variability and selecting reference sites. Classification of rivers and environmental health indicators, Proceedings of a Joint South African/Australian Workshop. -Water Research Commission, pp.129-166, 1994.

R. H. Norris, S. Linke, I. Prosser, W. J. Young, P. Liston et al.,

M. Thoms, Very-broad-scale assessment of human impacts on river condition, Freshwater Biology, vol.52, pp.959-976, 2007.

M. J. Novacek and E. E. Cleland, The current biodiversity extinction event: Scenarios for mitigation and recovery, Proceedings of the National Academy of Sciences, vol.98, pp.5466-5470, 2001.

N. A. O'-connor, Quantification of submerged wood in a lowland Australian stream system, Freshwater Biology, vol.27, pp.387-395, 1992.

M. T. O'hare, A. Baattrup-pedersen, R. Nijboer, K. Szoszkiewicz, and T. Ferreira, , 2006.

, Macrophyte communities of European streams with altered physical habitat, Hydrobiologia, vol.566, pp.197-210

M. P. O'neil and A. D. Abrahams, Objective identification of pools and riffles, Water Resources Research, vol.20, pp.921-926, 1984.

T. Oberdorff and R. M. Hughes, Modification of an index of biotic integrity based on fish assemblages to characterize rivers of the Seine-Normandie basin, Hydrobiologia, vol.228, pp.117-130, 1992.

T. Oberdorff, D. Pont, B. Hugueny, and J. Porcher, Development and validation of a fish-based index for the assessment of 'river health' in France, Freshwater Biology, vol.47, pp.1720-1734, 2002.

D. M. Olson and E. Dinerstein, The Global 200: a representation approach to conserving the earth's most biologically valuable ecoregions, Conservation Biology, vol.12, pp.502-512, 1998.

L. L. Osborne and D. A. Koviacic, Riparian vegetated buffer strips in water-quality restoration and stream management, Freshwater Biology, vol.29, pp.243-258, 1993.

M. Parsons and R. H. Norris, The effect of habitat-specific sampling on biological assessment of water quality using a predictive model, Freshwater Biology, vol.36, pp.419-434, 1996.

. Bibliographie,

B. Passauer, P. Meilinger, A. Melzer, and S. Schneider, Does the structural quality of running waters affect the occurrence of macrophytes? Acta Hydrochimica et Hydrobiologica, vol.30, pp.197-206, 2002.

H. M. Pereira and D. H. Cooper, Towards the global monitoring of biodiversity change, TRENDS in Ecology and Evolution, vol.21, pp.123-129, 2006.

O. L. Petchey, A. L. Downing, G. G. Mittelbach, L. Persson, F. Christopher et al., Species loss and the structure and functioning of multitrophic aquatic systems, Oikos, vol.104, pp.467-478, 2004.

O. L. Petchey and K. J. Gaston, Functional diversity (FD), species richness, and community composition, Ecology Letters, vol.5, pp.402-411, 2002.

O. L. Petchey, J. Kevin, and K. J. Gaston, Functional diversity: back to basics and looking forward, Ecology Letters, vol.9, pp.741-758, 2006.

G. Petts and C. Amoros, Fluvial Hydrosystems, 1996.

G. E. Petts, Impounded Rivers: Perspectives for Ecological Management, 1984.

G. E. Petts, Regulated rivers in the United Kingdom, vol.2, pp.201-220, 1988.

G. L. Phillips, D. Eminson, and B. Moss, A mechanism to account for macrophyte decline in progressively eutrophicated freshwaters, Aquatic Botany, vol.4, pp.103-126, 1978.

B. Picon and . Le-citoyen, Sciences de la nature, sciences de la société. Les passeurs de frontières, p.590, 1992.

E. C. Pielou, The Interpretation of Ecological Data, 1984.

S. L. Pimm, G. J. Russell, J. L. Gittleman, and T. M. Brooks, The future of biodiversity, Science, vol.269, pp.347-350, 1995.

L. C. Pinder, A. F. Marker, R. H. Mann, J. A. Bass, and G. H. Coop, The River Ouse, a highly eutrophic, slow-flowing, regulated, lowland river in Eastern England, Regulated Rivers: Research and Management, vol.13, pp.203-218, 1997.

P. Pinto, M. Morais, M. Ilhéu, and L. Sandin, Relationships among biological elements (macrophytes, macroinvertebrates and ichthyofauna) for different core river types across Europe at two different spatial scales, Hydrobiologia, vol.566, pp.75-90, 2006.

N. L. Poff, Landscape filters and species traits: towards mechanistic understanding and prediction in stream ecology, Journal of the North American Benthological Society, vol.16, pp.391-409, 1997.

B. Pot and R. , Monitoring watercourse vegetation, a synecological approach to dynamic gradients, Hydrobiologia, vol.340, pp.59-65, 1996.

R. B. Primack, Essentials of conservation biology, 1993.

M. Proulx, F. R. Pick, P. B. Hamilton, and D. R. Lean, Experimental evidence for interactive impacts of human activities on lake algal species richness, Oikos, vol.76, pp.191-195, 1996.

J. Prygiel, La place de la biodiversité dans les réseaux de surveillance des eaux continentales françaises, Océanis, vol.25, pp.457-479, 1999.

J. Prygiel, P. Carpentier, and S. &. Almeida, Determination of the biological diatom index (IBD NF T 90-354): results of an intercomparison exercise, Journal of Applied Phycology, vol.14, pp.27-39, 2002.

S. Puijalon and G. Bornette, Phenotypic plasticity and mechanical stress: biomass partitionning and clonal growth of an aquatic plant species, American Journal of Botany, vol.93, pp.1090-1099, 2006.

S. Puijalon, G. Bornette, and P. Sagnes, Adaptations to increasing hydraulic stress: morphology, hydrodynamics and fitness of two higher aquatic plant species, Journal of Experimental Botany, vol.56, pp.777-786, 2005.
URL : https://hal.archives-ouvertes.fr/hal-00182525

K. Quednow and W. Püttmann, Monitoring terbutryn pollution in small rivers of Hesse, Germany. Journal of Environmental Monitoring, vol.9, pp.1337-1343, 2007.

R. B. Rader, A functional classification of the drift: traits that influence invertebrate availability to salmonids, Canadian Journal of Fisheries and Aquatic Sciences, vol.54, pp.1211-1234, 1997.

M. Rambaud, Espèces typiques et Directive « Habitats ». Définition et utilisation du concept dans le cadre de l'évaluation de l'état de conservation des habitats naturels, pp.1-45, 2005.

J. Rameau, De la typologie CORINE biotopes aux habitats visés par la directive européenne 92/43/CEE, Le réseau Natura 2000 en France et dans les pays de l'union européenne et ses objectifs, pp.57-63, 2000.

J. Rameau, Données de l' IFN et habitats forestiers = NFI data and forest habitats, Revue Forestière Française, vol.53, pp.359-364, 2001.

C. R. Rao, Diversity and dissimilarity coefficients: a unified approach, Theorical Population Biology, vol.21, pp.24-43, 1982.

D. J. Rapport, Ecosystem behavior under stress, American Naturalist, vol.125, pp.617-640, 1985.

B. Rapport, D. J. Gaudet, C. Karr, J. R. Baron, J. S. Bohlen et al., Evaluating landscape health: integrating societal goals and biophysical processes, Journal of Environmental Management, vol.53, pp.1-15, 1998.

D. J. Rapport, C. Thorpe, and H. A. Regier, Ecosystem medicine, Bulletin of the Ecological Society of America, vol.60, pp.180-182, 1979.

S. R. Reice, Nonequilibrium determinants of biological community structure, AMerican Scientist, vol.82, pp.424-435, 1994.

W. V. Reid, How many species will there be?, Tropical Deforestation and Species Extinction, 1992.

V. H. Resh, A. G. Hildrew, B. Statzner, and C. R. Townsend, Theoretical habitat templets, species traits, and species richness: a synthesis of long-term ecological research on the Upper Rhône River in the context of concurrently developed ecological theory, Freshwater Biology, vol.31, pp.539-554, 1994.

T. B. Reynoldson, R. C. Bailey, K. E. Day, and R. H. Norris, Biological guidelines for freshwater sediment based on BEnthic Assessment of SedimenT (the BEAST) using a multivariate approach for predicting biological state, Australian Journal of Ecology, vol.20, pp.198-219, 1995.

T. B. Reynoldson, K. E. Day, and T. Pascoe, The development of the BEAST: a predictive approach for assessing sediment quality in the Great Lakes, 2000.

D. W. Sutcliffe and M. T. Furse, Assessing the Biological Quality of Freshwaters: RIVPACS and Similar Techniques, pp.165-180

A. Ricciardi and J. B. Rasmussen, Extinction Rates of North American Freshwater Fauna, Conservation Biology, vol.13, pp.1220-1222, 1999.

C. Richards, R. J. Haro, L. B. Johnson, and G. E. Host, Catchment and reach-scale properties as indicators of macroinvertebrate species traits, Freshwater Biology, vol.37, pp.219-230, 1997.

C. Ricotta, From theoretical ecology to statistical physics and back: self-similar landscape metrics as a synthesis of ecological diversity and geometrical complexity, Ecological Modelling, vol.125, pp.245-253, 2000.

D. F. Ritter, The effects of channelization on a high energy river, Environmental Geology, vol.3, pp.29-38, 1979.

F. Bibliographie-robach, I. Eglin, and R. Carbiener, Hydrosystème rhénan: évolution parallèle de la végétation aquatique et de la qualité de l' eau (Rhinau), Bulletin d' Ecology, vol.22, pp.227-241, 1991.

F. Robach, I. Eglin, and M. Trémolières, Species richness of aquatic macrophytes in former channels connected to a river: a comparison between two fluvial hydrosystems differing in their regime and regulation, Global ecology and biogeography letters, vol.6, pp.267-274, 1997.

F. Robach, G. Thiébaut, M. Trémolières, and S. Muller, A reference system for continental running waters: Plant communities as bioindicators of increasing eutrophication in alkaline and acidic waters in north east France, Hydrobiologia, vol.340, pp.67-76, 1996.

B. Rorslett and S. W. Johansen, Remedial measures connected with aquatic macrophytes in Norweigian regulated rivers and reservoirs, Regulated Rivers: Research and Management, vol.12, pp.509-522, 1996.

D. M. Rosemberg, P. Mccully, and C. M. Pringle, Global-scale environmental effects of hydrological alternations: introduction, Bioscience, vol.50, pp.746-751, 2000.

D. M. Rosenberg and V. H. Resh, Introduction to freshwater biomonitoring and benthic macroinvertebrates, Freshwater Biomonitoring and Benthic Macroinvertebrates, pp.1-9, 1993.

D. M. Rosenberg, T. B. Reynoldson, and V. H. Resh, Establishing reference conditions in the Fraser River catchment, British Colombia, Canada, using the BEAST (Benthic Assessment of SedimenT) predictive model, 2000.

M. T. Furse, Assessing the Biological Quality of Freshwaters: RIVPACS and Similar Techniques, pp.181-194

N. E. Roth, J. D. Allan, and D. L. Erickson, Landscape influences on stream biotic integrity assessed at multiple spatial scales, Landscape Ecology, vol.11, pp.141-156, 1996.

S. P. Rushton, D. Hill, and S. P. Carter, The abundance of river corridor birds in relation to their habitats: a modelling approach, Journal of Applied Ecology, vol.31, pp.313-328, 1994.

S. Sabater, Diatom communities as indicators of environmental stress in the Guadiamar River, S.-W. Spain, following a major mine tailings spill, Journal of Applied Phycology, vol.12, pp.113-124, 2000.

J. L. Sabo, R. Sponseller, M. Dixon, K. Gade, T. Harms et al., Riparian zones increase regional species diversity by harboring different, not more, species, Ecology, vol.86, pp.56-62, 2005.

O. E. Sala, F. S. Chapin, J. J. Armesto, E. Berlow, J. Bloomfield et al.,

M. Oesterheld, N. L. Poff, M. T. Sykes, B. H. Walker, M. Walker et al., , 2000.

, Global Biodiversity Scenarios for the Year 2100, Science, vol.287, pp.1770-1774

K. Sand-jensen, Influence of submerged macrophytes on sediment composition and near-bed flow in lowland streams, Freshwater Biology, vol.39, pp.663-679, 1998.

K. Sand-jensen, D. Borg, and E. Jeppesen, Biomass and oxygen dynamics of the epiphytic community in a Danish lowland stream, Freshwater Biology, vol.22, pp.431-443, 1989.

K. Sand-jensen and J. R. Mebus, Fine-scale patterns of water velocity within macrophyte patches in streams, Oikos, vol.76, pp.169-180, 1996.

J. Schaumburg, C. Schranz, J. Foerster, A. Gutowski, G. Hofmann et al., Ecological classification of macrophytes and phytobenthos for rivers in Germany according to the Water Framework Directive, Limnologica, vol.34, pp.283-301, 2004.

S. Schneider, T. Krumpholz, and A. Melzer, Trophieindikation in Fließgewässern mit Hilfe des TIM (Trophie-Index Macrophyten) -Erprobung eines neu entwickelten Index im Inniger Bach, Acta Hydrochimica Hydrobiologica, vol.28, pp.241-249, 2000.

M. Schulz and B. Gücker, Macrophytes Increase Spatial Patchiness of Fluvial Sedimentary Records and Effect Temporal Particulate Nutrient Storage, Aquatic Geochemistry, vol.11, pp.89-107, 2005.

J. Scullion, C. A. Parish, N. Morgan, and R. W. Edwards, Comparison of benthic macroinvertebrate fauna and substratum composition in riffles and pools in the impounded River Elan and the unregulated River Wye, mid-Wales, Freshwater Biology, vol.12, pp.579-595, 1982.

C. D. Sculthorpe, The Biology of Aquatic Vascular Plants, 1967.

V. E. Shelford, The ecology of North America, The Moss Flora of Britain and Ireland, 1963.

A. J. Smith, The Liverworts of Britain and Ireland, 1990.

C. D. Snyder, J. A. Young, R. Villella, and D. P. Lemarié, Influences of upland and riparian land use patterns on stream biotic integrity, Landscape Ecology, vol.18, pp.647-664, 2003.

M. E. Soule, Conservation biology and the real world, Conservation Biology -the Science of Scarcity and Diversity. -Sinauer Associates, pp.1-13, 1986.

M. E. Soule and G. O. Orians, Introduction, Conservation biology ; research priorities for the next decade. -Society for conservation biology, p.307, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00001348

M. E. Soule and B. A. Wilcox, Conservation biology : its scope and its challenge, Conservation biology : an evolutionary-ecological perspective. -Sinauer Associates, pp.1-9, 1980.

R. E. Sparks, Need for ecosystem management of large rivers and their floodplains, Bioscience, vol.45, pp.168-182, 1995.

C. Stalnaker, The use of habitat structure preferenda for establishing flow regimes necessary for maintenance of fish habitat, The Ecology of Regulated Streams, 1979.

B. Statzner, B. Bis, and P. Usseglio-polatera, Perspectives for biomonitoring at large spatial scales: a unified measure for the functional composition of invertebrate communities in European running waters, Basic and Applied Ecology, vol.1, pp.73-85, 2001.

B. Statzner and B. Higher, Stream hydraulics as a major determinant of benthic invertebrate zonation patterns, Freshwater Biology, vol.16, pp.127-139, 1986.

A. D. Steinman, P. J. Mulholland, and W. R. Hill, Functional responses associated with growth form in stream algae, Journal of the North American Benthological Society, vol.11, pp.229-243, 1992.

J. ?tirn, Manual of methods in aquatic environment research. Part 8. Ecological assessment of pollution effects. FAO Fisheries Technical Paper 209, p.71, 1992.

R. A. Sweeting, River Pollution, The Rivers Handbook. -Blackwell Scientific, pp.23-32, 1994.

, Diagnostic de la qualité piscicole de la rivière Ecole et de ses affluents, pp.1-33, 2005.

K. Szoszkiewicz, T. Ferreira, T. Korte, A. Baattrup-pedersen, J. Davy-bowker et al., European river plant communities: the importance of organic pollution and the usefulness of existing macrophyte metrics, Hydrobiologia, vol.566, pp.211-234, 2006.

. Bibliographie,

C. R. Townsend and R. H. Riley, Assessment of river health: accounting for perturbation pathways in physical and ecological space, Freshwater Biology, vol.41, pp.393-405, 1999.

M. Trémolières, U. Roeck, J. Klein, and R. Carbiener, The exchange process between river and groundwater on the Central Alsace floodplain (Eastern France). I. The case of a river with functional floodplain, Hydrobiologia, vol.273, pp.19-36, 1993.

H. Tremp and A. Kohler, The usefulness of macrophyte monitoring-systems, exemplified on eutrophication and acidification of running waters, Acta Botanica Gallica, vol.142, pp.541-550, 1995.

T. G. Tutin, V. H. Heywood, N. A. Burges, D. M. Moore, D. H. Valentine et al.,

D. H. Webb, Flora Europea, 1964.

. Van-dam, A coded checklist and ecological indicator values of freshwater diatoms from the Netherlands, Netherlands Journal of Aquatic Ecology, vol.28, pp.117-133, 1994.

R. L. Vannote, G. W. Minshall, K. W. Cummins, J. R. Sedell, and C. E. Cushing, The river continuum concept, Canadian Journal of Fisheries and Aquatic Sciences, vol.37, pp.130-137, 1980.

J. &. Verneaux, Une nouvelle méthode pratique d'évaluation de la qualité des eaux courantes -Un indice biologique de qualité générale (I, Annales Scientifiques de l' Université, vol.4, pp.11-19, 1982.

J. Verneaux, J. P. Vergoin, and M. Larinier, Aspects écologiques des travaux d' aménagement des cours d' eau. La Houille Blanche 2-3, pp.127-131, 1975.

B. Wallace and N. H. Anderson, Habitat, life history, and behavioral adaptations of aquatic insects, pp.41-73, 1996.

J. V. Ward, Riverine landscapes: biodiversity patterns, disturbance regimes, and aquatic conservation, Biological Conservation, vol.83, pp.269-278, 1998.

J. V. Ward and J. A. Stanford, The Ecology of Regulated Streams, 1979.

J. V. Ward, K. Tockner, P. J. Edwards, J. Kollmann, G. Bretschko et al., A reference river system for the Alps: the "Fiume tagliamento, vol.15, pp.63-75, 1999.

R. M. Warwick and K. R. Clarke, A comparison of some methods for analysing changes in benthic community structure, Journal of the Marine Biological Association of the United Kingdom, pp.225-244, 1991.

J. G. Wasson, J. R. Malavoi, L. Maridet, Y. Souchon, and L. Paulin, Impacts écologiques de la chenalisation des rivières, série Gestion des Milieux Aquatiques, 1995.

J. R. Webster, M. E. Gurtz, J. J. Hains, J. L. Meyer, W. T. Swank et al., Stability of stream ecosystems, Stream Ecology: Applications and Testing of General Ecological Theory, pp.355-395, 1983.

D. F. Westlake, Macrophytes, River ecology, pp.106-128, 1975.

P. S. White and S. T. Pickett, Natural disturbance and patch dynamics: an introduction, The Ecology of Natural Disturbance and Patch Dynamics, p.172, 1985.

J. A. Wiens, Riverine landscapes: taking landscape ecology into the water, Freshwater Biology, vol.47, pp.501-515, 2002.

O. Wildi, E. Feldmeyer-christe, R. Ghosh, and N. E. Zimmermann, Comments on vegetation monitoring approaches, Community Ecology, vol.5, pp.1-6, 2004.

N. J. Willby, V. J. Abernethy, and B. O. Demars, Attribute-based classification of European hydrophytes and its relationship to habitat utilization, Freshwater Biology, vol.43, pp.43-74, 2000.

J. F. Wright, Development and use of a system for predicting the macroinvertebrate fauna in flowing waters, Australian Journal of Ecology, vol.20, pp.181-197, 1995.

J. F. Wright, P. D. Armitage, and M. T. Furse, Prediction of invertebrate communities using stream measurements, Regulated Rivers: Research and Management, vol.4, pp.147-155, 1989.

R. H. Yapp, Annexes Eutrophe : se dit d' un milieu de capacité nutritive riche à très riche, c'est-à-dire riche en nutriments, Journal of Ecology, vol.10, pp.1-17, 1922.

, Eutrophisation : enrichissement de l' eau, qu' elle soit douce ou saline, par des nutriments, en particulier par des composés d' azote et de phosphore, qui accélèrent la croissance d' algues et des formes plus développées de la vie végétale

, de la surface de l'eau, et des distributions des hauteurs d'eau, des vitesses du courant, et de la granulométrie du substrat. La longueur d'un faciès peut varier d'une à quelques fois la largeur du lit mouillé. A titre d'exemple, on peut citer trois grands types de faciès contrastés : les mouilles (pente relativement faible, fortes hauteurs d'eau, faibles vitesses), les rapides (pente élevée, fortes vitesses du courant, substrat composé majoritairement de gros blocs) et les plats (pente moyenne, vitesses moyennes et uniformes, hauteurs d'eau plutôt faibles

C. Lyon,

, Granulométrie : répartition des éléments selon leur taille

, Hélophyte : plante intermédiaire entre les types terrestre et aquatique, qui vit principalement dans les marécages gorgés d' eau, ou dans l' eau elle-même d' où émergent les rameaux portant feuilles et fleurs. Plante aquatique ou semi-aquatique pérenne adaptée aux espaces marécageux

, Hydrologie : étude des variations spatiales et temporelles du débit des cours d'eau

, Hydrophyte : plante qui croît dans l' eau et les sols saturés. Plante cryptophyte qui survit, pendant la saison la moins favorable à sa croissance