The basin of Thau in southern France is a shallow, weakly flushed lagoon which is an important location for oyster cultivation. Phytoplankton analyses were carried out in 1975-1976 and then (almost) continuously since 1987. We report an investigation of 'the balance of organisms' in phytoplankton in relation to reductions in phosphorus loading, using two new tools based on phytoplankton lifeforms: the Plankton Index for Phytoplankton (PIp); Euclidean distance in state space. Our results show the utility of the tools for analysing changes in the ‘balance of organisms’ at the level of functional groups (in our study diatoms and dinoflagellates), but also illustrate the difficulties in demonstrating the reversal of human impacts resulting from eutrophication. The comparison between 1987-89 and 1976 showed the expected 'de-eutrophication' due to the reduction in dissolved inorganic phosphate (DIP), with a decrease in dinoflagellate abundance. Since 1989, year-to-year variation in annual mean concentrations of (DIP) may have contributed to inter-annual variability in the balance of the two lifeforms, but the data suggest that the system has remained in a dynamically stable regime because: (i) there was no long-term trend in Euclidean distance from the reference; and (ii) there was no increase in inter-annual variability about the time-series mean Euclidean distance suggesting there has been no decrease in resilience which might signal a regime change. Integrated management of human activities will be required to manage (and reduce) total P in the system. Monitoring phytoplankton and nutrients concentrations to determine how primary production and the balance of species respond to further changes in the nutrient status of the lagoon should be an integral part of any management programme.