Trends and seasonality analysis from 1980 onward and longitudinal distribution, from headwaters to estuary, of chlorophyll a, nitrate and phosphate were investigated in the eutrophic Loire River. The continuous decline of phosphate concentrations which has been recorded since 1991 both in the main river and in the tributaries has led to the conclusion that it was responsible for the significant reduction in phytoplanktonic biomass across the whole river system, although Corbicula spp. clams invaded the river during the same period and probably played a significant role in the phytoplankton decline. While eutrophication remained lower in the main tributaries than in the Loire itself, they were found to contribute up to ≈ 35% to the total nutrient load of the main river. The seasonality analysis revealed significant seasonal variations for the different eutrophication metrics and calls into question the classical monthly survey recommended by national or international authorities. Reducing P inputs impacted these seasonal variations: the decline of seasonal amplitudes of chlorophyll a reduced the seasonal amplitude of orthophosphate and of daily variations of dissolved oxygen and pH but did not significantly affect the seasonal amplitude of nitrate. Thus, the influence of phytoplankton on seasonal variations of nitrate was minor throughout the period of study.