European freshwater ecosystems have undergone significant human-induced and environmentally-driven variations in nutrient export from catchments throughout the past five decades, mainly in connection with changes in land-use, agricultural practice, waste water production and treatment, and climatic conditions. We analysed the relations among concentration of total phosphorus (TP) in the Slapy Reservoir (a middle reservoir of the Vltava River Cascade, Czechia), and socio-economic and climatic factors from 1963 to 2015. The study was based on a time series analysis, using conventional statistical tools, and the identification of breaking points, using a segmented regression. Results indicated clear long-term trends and seasonal patterns of TP, with annual average TP increasing up until 1991 and decreasing from 1992 to 2015. Trends in annual, winter and spring average TP concentrations reflected a shift in development of sewerage and sanitary infrastructure, agricultural application of fertilizers, and livestock production in the early 1990s that was associated with changes from the planned to the market economy. No trends were observed for average TP in autumn. The summer average TP has fluctuated with increased amplitude since 1991 in connection with recent climate warming, changes in thermal stratification stability, increased water flow irregularities, and short-circuiting of TP-rich inflow during high flow events. The climate-change-induced processes confound the generally declining trend in lake-water TP concentration and can result in eutrophication despite decreased phosphorus loads from the catchment. Our findings indicate the need of further reduction of phosphorus sources to meet ecological quality standards of the EU Water Framework Directive because the climate change may lead to a greater susceptibility of the aquatic ecosystem to the supply of nutrients.