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The implementation of a conservation program since the early 1980s resulted in a reduction in phosphorus concentrations in Lake Geneva. However, in the 1990s, phytoplankton biomass increased again, almost reaching the high values recorded during the period of greatest P loading. The structural changes in the phytoplankton of Lake Geneva over the past 25 yr have been analyzed using a recently developed statistical method based on hierarchical clustering and Bayesian probabilities. This method has been used to identify phytoplankton assemblages and to map annual and interannual successional patterns simultaneously. Characteristic species were identified for each cluster after calculation of their relative species fidelity and specificity indices. Six distinct phytoplankton assemblages were identified, and although the way species are organized into communities remains unclear, the seasonal patterns of succession are consistent with the C-S-R adaptive strategies and are characteristic of temperate lakes. This pattern broadly recurred over the years, but was markedly influenced by both human activity and regional climatic changes: The warmer winters and springs recorded in Europe since 1988 led to an earlier clear-water phase.

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Long‐term phytoplankton responses in Lake Geneva to a decline in phosphorus (P) loading are examined in terms of summer (July–September) biomass and community structure. With the rapid development of human activity on its banks and within its catchment area in the 1960s, this large subalpine hydrosystem shifted from oligotrophy to eutrophy within approximately one decade. Measures to reduce P loading were initiated successfully in the mid‐1970s, when total P concentrations in the winter overturn altered from 90 μg/L in 1980 to 40 μg/L in 1998. Until the 1990s, algal descriptors improved as expected (biomass decline, reappearance of diatom species, increased contribution of nanoplankton). Then, paradoxically, and in contrast to the reappearance of oligotrophic species, summer algal biomass began to increase. Pre‐summer (period prior to the beginning of the clear water phase) dissolved inorganic phosphorus concentrations and summer phytoplankton composition presented similar interannual trends. However, the succession of phytoplankton structure during the reoligotrophication phase differed greatly from that during the eutrophication period, and a recent abnormal upward trend in algal densities is mainly the result of the development of large species that formerly were only common from late September until November. This community change, mainly triggered by filamentous (Mougeotia gracillima, Tribonema) or motile forms (Dinobryon sociale, Cryptophycea), seems to have been induced by the earlier and greater deepening of the P‐depleted layer. In addition to milder summers, this massive development of larger forms seems to be favoured by four of their biological features: tolerance to warm temperatures, tolerance to low‐light intensity (might exploit deeper layers where P is not yet limiting), shapes not only providing a large surface to volume ratio or motility (adaptation to low‐nutrient concentrations), but increasing resistance to zooplankton grazing. This paradoxical trend, perhaps reinforced by the decline on roach Rutilus rutilus abundance (an opportunistic planktivore), is likely to remain until the P‐depleted zone is extended below the layers that can be frequently resupplied in nutrients by hydrodynamic processes.