Catchment lithologies and human activities can cause variations in riverine carbon (C), nitrogen (N), and phosphorus (P) loads, and the ratio of these nutrients may affect the primary productivity of rivers and their phytoplankton communities. We conducted a comparative study of biogeochemical variations in three major European rivers—the Rhine, Danube, and Seine—which reveals the impacts of different carbonate outcrops and human impacts (agricultural activities and sewage input) on the changes in the limiting nutrients and phytoplankton community compositions of flowing water systems. N limitation was observed in the Rhine and Danube owing to their low average NO₃^– loads (4.04–6.45 mg/L). Although the extensive outcrops of carbonate rocks in the Seine catchment result in high average HCO₃^– concentrations of ∼ 4.68 mmol/L, the elevated inorganic C input did not match the high average NO₃^– loads (∼19.38 mg/L), driven by intensive agricultural activity and urban sewage input, demonstrating a potential C limitation on productivity. Our results show that the productivity of the Seine River, determined by the chlorophyll-a concentration, was significantly related to the dissolved inorganic carbon (DIC) concentration (coefficient of determination: R² = 0.68, P < 0.05). Our results demonstrate that changes in DIC content can significantly alter the dominant phytoplankton species in the water column. The high inputs of DIC and aqueous CO_2(aq) to the Seine lead to Bacillariophyta proportions that are 3.96–8.81 % and 19.87–22.56 % higher than those of the Rhine and Danube in the wet and dry seasons, respectively. This can be explained by the difference in the efficiency of carbon concentrating mechanisms (CCMs) among phytoplankton species. Therefore, to mitigate river eutrophication and improve the quality of the aquatic environment, we suggest that future water–carbon management in the flowing water systems with abundant nutrients should consider C-limitation alleviation and its potential effect for reducing the abundance of harmful algae.