A two-year study was conducted to explore summer development of macroalgae and their total phosphorus and nitrogen content at three stations in a broad and clear French carbonate river. Water discharge, temperature and insolation, each with a different time lag, as well as substrates and nutrients were examined in order to explain macroalgal biomass variability. Twenty-four macroalgae genera were recorded with Spirogyra, Cladophora, Vaucheria and Oedogonium as abundant. Through redundancy analysis the macroalgal community composition exhibited significant differences, between the sampling sites and also from one year to the next. Water discharge (time-lag = 5 days) and temperature (time-lag = 20 days) both significantly explained macroalgal biomass variability, highlighting differences in the time lag of the macroalgal community's ecological response to environmental changes. Spatial segregation was observed within the wide riverbed due to habitat variability, allowing co-occurrence in the development of ecologically different taxa within each sampling site. The high nitrate concentrations as compared with the particular low phosphorus concentrations led to especially high DIN/SRP ratios (248 ± 103, n = 18). The N/P ratios in algal tissues were high (25 ± 16, n = 26) and indicated P-limitation. The differences in DIN/SRP and N/P ratios suggest additional nutrient sources than open water such as groundwater inputs.