, The Proliphyc project is funded by the ANR-PRECODD Programme We wish to acknowledge Pascal Perney (INRA) for the logistic support and Yannis Cuypers (LOCEAN, Université Pierre et Marie Curie) for fruitful discussions. The authors also express their gratitude

A. , Water quality -Guidance standard on the enumeration of phytoplankton using inverted microscopy (Utermöhl technique), 2006.

I. Allan, B. Vrana, R. Greenwood, G. Mills, B. Roig et al., A "toolbox" for biological and chemical monitoring requirements for the European Union's Water Framework Directive. Talanta 1st Swift-WFD workshop on validation of Robustness of sensors and bioassays for Screening Pollutants -1st SWIFT-WFD, pp.302-322, 2004.

O. Anneville, S. Gammeter, and D. Straile, Phosphorus decrease and climate variability: mediators of synchrony in phytoplankton changes among European peri-alpine lakes, Freshwater Biology, vol.9, issue.10, pp.1731-1746, 2005.
DOI : 10.1023/A:1018513530268

O. Anneville, V. Ginot, J. Druart, and N. Angeli, Long-term study (1974-1998) of seasonal changes in the phytoplankton in Lake Geneva: a multi-table approach, Journal of Plankton Research, vol.24, issue.10, pp.993-1008, 2002.
DOI : 10.1093/plankt/24.10.993

N. Bensoussan, M. Calzas, Y. Degres, C. Drezen, N. Escoffier et al., Observing and integrating deep chlorophyll maximum of the metalimnetic cyanobacteria P.rubescens from single point measurements In: ASLO Aquatic Science Meeting Abstracts, From in Situ Time Series to Mean Image: new Tools for Monitoring Harmful Algal Blooms. In: AGU fall meeting Geophysical research abstracts WL. 2005. Time-series observations during the low sub-surface oxygen events in Narragansett Bay during summer, pp.90-103, 2001.

M. Beutler, K. Wiltshire, B. Meyer, C. Moldaenke, C. Lüring et al., A fluorometric method for the differentiation of algal populations in vivo and in situ, Photosynthesis Research, vol.72, issue.1, pp.39-53, 2002.
DOI : 10.1023/A:1016026607048

S. Blain, J. Guillou, P. Treguer, P. Woerther, L. Delauney et al., High frequency monitoring of the coastal marine environment using the MAREL buoy, J. Environ. Monit., vol.29, issue.2, pp.569-575, 2004.
DOI : 10.4319/lo.1984.29.3.0620

P. Bournet, D. Dartus, . Tassin, and B. Et-vinçon-leite, , pp.247-266, 1996.

J. Briand, S. Jacquet, C. Flinois, C. Avois-jacquet, C. Maisonnette et al., Variations in the Microcystin Production of Planktothrix rubescens (Cyanobacteria) Assessed from a Four-Year Survey of Lac du Bourget (France) and from Laboratory Experiments, Microbial Ecology, vol.69, issue.Suppl, pp.418-428, 2005.
DOI : 10.1127/archiv-hydrobiol/155/2002/383

S. Bricker, J. Ferreira, and T. Simas, An integrated methodology for assessment of estuarine trophic status, Ecological Modelling, vol.169, issue.1, pp.39-60, 2003.
DOI : 10.1016/S0304-3800(03)00199-6

J. Carstensen, . Cereve, I. Greti, and C. , Statistical principles for ecological status classification of Water Framework Directive monitoring data Marine Pollution Bulletin Implementation of the Water Framework Directive in European marine waters 55:3-15 Toxic Cyanobacteria in Water: a guide to their public health consequences, monitoring and management, Analyse de l'évolution de la qualité des eaux du lac du Bourget Chambéry: CISALB. p 310. Chorus I, Bartram J, 1995.

Y. Cuypers, B. Vinçon-leite, M. Poulin, B. Tassin, B. Vinçon-leite et al., Non linear internal seiches degeneration in a in a deep sub-alpine Internal wave dynamics in a deep subalpine lake, from basin scale seiches to nonlinear high frequency waves, Proceedings of the 10 th european workshop on physical processes in natural waters. Granada, Spain. Cuypers Y Ondes internes et mélange turbulent dans le lac du Bourget, pp.1-12, 2006.

M. Dokulil and K. Teubner, Do phytoplankton communities correctly track trophic changes? An assessment using directly measured and palaeolimnological data, Freshwater Biology, vol.31, issue.10, pp.1594-1604, 2005.
DOI : 10.1023/B:HYDR.0000004269.54705.cb

U. Dorigo, D. Fontvieille, and J. Humbert, Spatial variability in the abundance and composition of the free-living bacterioplankton community in the pelagic zone of Lake Bourget (France), FEMS Microbiology Ecology, vol.70, issue.1, pp.109-119, 2006.
DOI : 10.1007/978-94-015-7358-0

G. Dur, F. Schmitt, and S. Souissi, Analysis of high frequency temperature time series in the Seine estuary from the Marel autonomous monitoring buoy, Hydrobiologia, vol.21, issue.48, pp.59-68, 2007.
DOI : 10.5194/npg-3-247-1996

URL : https://hal.archives-ouvertes.fr/hal-00481719

T. Dworak, C. Gonzalez, C. Laaser, and E. Interwies, The need for new monitoring tools to implement the WFD. Environmental Science & Policy Research & Technology Integration in Support of the European Union Water Framework Directive Water Framework Directive Monitoring Programme, pp.301-306, 2005.
DOI : 10.1016/j.envsci.2005.03.007

B. Ernst, S. Hoeger, O. Brien, E. Dietrich, and D. , Oral toxicity of the microcystin-containing cyanobacterium Planktothrix rubescens in European whitefish (Coregonus lavaretus), Aquatic Toxicology, vol.79, issue.1, pp.31-40, 2006.
DOI : 10.1016/j.aquatox.2006.04.013

B. Ernst, S. Hoeger, O. Brien, E. Dietrich, and D. , Abundance and toxicity of Planktothrix rubescens in the pre-alpine Lake Ammersee, Germany, Harmful Algae, vol.8, issue.2, pp.329-342, 2009.
DOI : 10.1016/j.hal.2008.07.006

E. Parliament, C. Ferreira, J. Vale, C. Soares, C. Salas et al., DirectiveEC of the European Parliament and of the Council of 23 October 2000 establishing a framework for Community action in the field of water policy, Monitoring of coastal and transitional waters under the E.U. Water Framework Directive, pp.195-216, 2000.

J. Feuillade and A. Orand, Studies on Lake Nantua. Lake surroundings and historical background. Studies on Lake Nantua (France) A Eutrophic Lake on the Way to Rehabilitation, Arch. Hydrobiol. Beih. Ergebn. Limnol, vol.42, pp.1-16, 1994.

E. Garel, S. Nunes, J. Neto, R. Fernandes, R. Neves et al., The autonomous Simpatico system for real-time continuous water-quality and current velocity monitoring: examples of application in three Portuguese estuaries, Geo-Marine Letters, vol.24, issue.2/4, pp.331-341, 2009.
DOI : 10.1002/joc.1048

D. Gerdeaux, O. Anneville, and D. Hefti, Fishery changes during re-oligotrophication in??11??peri-alpine Swiss and??French lakes over the??past 30??years, Acta Oecologica, vol.30, issue.2, pp.161-167, 2006.
DOI : 10.1016/j.actao.2006.02.007

A. Groleau, G. Sarazin, B. Vinçon-leite, B. Tassin, and C. Quiblier-lloberas, Tracing calcite precipitation with specific conductance in a hard water alpine lake (Lake Bourget), Water Research, vol.34, issue.17, pp.4151-4160, 2000.
DOI : 10.1016/S0043-1354(00)00191-3

URL : https://hal.archives-ouvertes.fr/hal-00711823

B. Henderson-sellers, Engineering limnology, 1984.

D. Holland and A. Walsby, in the cold and dark, related to over-winter survival and summer recruitment in Lake Z??rich, European Journal of Phycology, vol.65, issue.2, pp.179-184, 2008.
DOI : 10.1046/j.1365-2427.2003.01134.x

URL : http://www.tandfonline.com/doi/pdf/10.1080/09670260801904822?needAccess=true

H. K. Hudnell, The state of U.S. freshwater harmful algal blooms assessments, policy and legislation, Toxicon, vol.55, issue.5
DOI : 10.1016/j.toxicon.2009.07.021

J. Humbert, G. Paolini, and B. Leberre, Monitoring a toxic cyanobacterial bloom in Lake Bourget (France) and its consequences for water quality, Proceedings of the 9 th International Conference on Harmful Algal Blooms. Hobart, Australia: G. Hallegraeff et al. p 496-499. INSEE. 2008. Recensement de la population en France, 2000.

G. Jann-para, I. Schwob, and M. Feuillade, Occurrence of toxic Planktothrix rubescens blooms in lake Nantua, France, Toxicon, vol.43, issue.3, pp.279-285, 2004.
DOI : 10.1016/j.toxicon.2003.12.005

URL : https://hal.archives-ouvertes.fr/hal-01769386

E. Jeppesen, M. Søndergaard, J. P. Jensen, K. E. Havens, O. Anneville et al., Lake responses to reduced nutrient loading - an analysis of contemporary long-term data from 35 case studies, Freshwater Biology, vol.5, issue.10, pp.1747-1771, 2005.
DOI : 10.1007/BF00000968

I. Jones and S. Maberly, Automatic in-lake monitoring in the English Lake District: The effect of lake size on stratification, SIL Proceedings, 1922-2010, vol.45, issue.1, pp.70-72, 2008.
DOI : 10.4319/lo.2000.45.6.1388

C. Kaiblinger, O. Anneville, R. Tadonleke, F. Rimet, J. Druart et al.,

, Central European water quality indices applied to long-term data from peri-alpine lakes: test and possible improvements, Hydrobiologia, vol.633, pp.67-74

J. Lee, I. Hodgkiss, K. Wong, and I. Lam, Real time observations of coastal algal blooms by an early warning system, Estuarine, Coastal and Shelf Science, vol.65, issue.1-2, pp.172-190, 2005.
DOI : 10.1016/j.ecss.2005.06.005

U. Lemmin and C. Mortimer, Tests of an extension to internal seiches of Defant's procedure for determination of surface seiche characteristics in real lakes1, Limnology and Oceanography, vol.31, issue.6, pp.1207-1231, 1986.
DOI : 10.4319/lo.1986.31.6.1207

G. Madgwick, I. Jones, S. Thackeray, J. Elliott, H. Miller et al., Phytoplankton communities and antecedent conditions: high resolution sampling in Esthwaite Water, Building the European Capacity in Operational Oceanography, Proceedings, pp.1798-1810, 2003.
DOI : 10.1139/cjfas-53-3-621

. Ministère-de-l-'ecologie, D. Du, and . Durable, Circulaire relative à la constitution et la mise en oeuvre du programme de surveillance pour les eaux douces de surface en application de la directive, 2000.

L. Oberhaus, A. Groleau, C. Quiblier-lloberas, J. Druart, B. Vinçon-leite et al., Influence of physical factors on Cyanobacteria development in a deep subalpine lake (Lake Bourget), 2003.

P. Oberholster, A. Botha, T. Cloete, M. Devlin, S. Rogers et al., Toxic cyanobacterial blooms in a shallow, artificially mixed urban lake in Colorado, USA. Lakes and Reservoirs: Research and Management Eutrophication of waters : monitoring, assessment and control Assessing the suitability of OSPAR EcoQOs for eutrophication vs ICES criteria for England and Wales, Paris. Painting SJ Marine Pollution Bulletin, vol.11, issue.50, pp.111-1231569, 1982.
DOI : 10.1111/j.1440-1770.2006.00297.x

B. Palethorpe, B. Hayes-gill, J. Crowe, M. Sumner, N. Crout et al., Real-time physical data acquisition through a remote sensing platform on a polar lake, Limnology and Oceanography: Methods, vol.2, issue.6, pp.191-201, 2004.
DOI : 10.4319/lom.2004.2.191

URL : http://onlinelibrary.wiley.com/doi/10.4319/lom.2004.2.191/pdf

G. Paolini, F. Chambéry, N. Salmaso, G. Morabito, F. Buzzi et al., Phytoplankton as an Indicator of the Water Quality of the Deep Lakes South of the Alps, Colloque "Autour du lac du Bourget, pp.167-187, 2006.

H. Sarmento and J. Descy, Use of marker pigments and functional groups for assessing the status of phytoplankton assemblages in lakes, Journal of Applied Phycology, vol.18, issue.6, pp.1001-1011, 2008.
DOI : 10.1016/S0075-9511(04)80048-3

R. D. Tadonleke, J. Lazzarotto, O. Anneville, and J. C. Druart, Phytoplankton productivity increased in Lake Geneva despite phosphorus loading reduction, Journal of Plankton Research, vol.24, issue.8, pp.1179-1194, 2009.
DOI : 10.1579/0044-7447-30.8.529

URL : https://academic.oup.com/plankt/article-pdf/31/10/1179/4378700/fbp063.pdf

B. Tassin, B. Vinçon-leite, M. Tilzer, U. Gaedke, A. Schweizer et al., Forecasting of water quality in lakes: a predictive use of a onedimensional model Application to lake Bourget Interannual Variability of Phytoplankton Productivity and Related Parameters in Lake Constance -No Response to Decreased Phosphorus Loading, Hydrobiologia Journal of Plankton Research, vol.374, issue.13, pp.47-60755, 1991.

V. Vandenberghe, P. L. Goethals, A. Van-griensven, J. Meirlaen, N. De-pauw et al., Application of Automated Measurement Stations for Continuous Water Quality Monitoring of the Dender River in Flanders, Belgium, Environmental Monitoring and Assessment, vol.485, issue.4, pp.85-98, 2005.
DOI : 10.1016/S0048-9697(96)05356-9

B. Vinçon-leite, J. Mouchel, and B. Tassin, Modelling the seasonal evolution of temperature in lake Bourget (France), Revue des sciences de l'eau, vol.2, issue.4, pp.483-510, 1989.
DOI : 10.7202/705040ar

B. Vinçon-leite, B. Tassin, and J. Druart, Phytoplankton variability in Lake Bourget: Phytoplankton dynamics and meteorology Lakes & Reservoirs, JM. 1995a. Contribution of Mathematical-Modeling to Lake Ecosystem Understanding -Lake Bourget, pp.93-102433, 2002.

A. Walsby, F. Schanz, and M. Schmid, The Burgundy-blood phenomenon: a model of buoyancy change explains autumnal waterblooms by Planktothrix rubescens in Lake Zurich, New Phytologist, vol.31, issue.1, pp.109-122, 2006.
DOI : 10.1046/j.1469-8137.2002.00401.x

A. Walsby and F. Schanz, Light-dependent growth rate determines changes in the population of Planktothrix rubescens over the annual cycle in Lake Z??rich, Switzerland, New Phytologist, vol.31, issue.3, pp.671-687, 2002.
DOI : 10.1007/PL00001358