The phytoplankton compartment is particularly reactive to changes in nutrient concentration and is used as a quality indicator. Using a simple numerical approach, the response of emblematic harmful taxa from the eastern English Channel and southern North Sea to changes in nutrient inputs was studied. The method is based on a diachronic approach using averaged maxima over sliding periods of six years (1994–2018). This gave a final dataset containing pairs of points (number of years) for explained and explanatory variables. The temporal trajectory of the relationship between each pair of variables was then highlighted. Changes were represented as long-term trajectories that allowed a comparison to a reference/average situation. In addition, the relevance of the use of Phaeocystis globosa and the Pseudo-nitzchia complex as eutrophication species indicators was tested. Results showed a significant shift in the 2000s and different trajectories between diatoms and P. globosa abundances in response to changes in Dissolved Inorganic Nitrogen (DIN). The contrasting ecosystems under study reacted differently depending on the initial pressure. While a return to good ecological status does not seem feasible in the short term, it seems that these ecosystems were in an unstable intermediate state requiring continued efforts to reduce nutrient inputs.