Over the past half-century, drastically increased chemical fertilizers have entered agricultural ecosystems to promote crop production on the Yangtze Plain, potentially enhancing agricultural nutrient sources for eutrophication in freshwater ecosystems. However, long-term trends of nitrogen dynamics in terrestrial ecosystems and their impacts on eutrophication changes in this region remain poorly studied. Using a process-based ecosystem model, we investigated the temporal and spatial patterns of nitrogen use efficiency (NUE) and nitrogen leaching on the Yangtze Plain from 1979–2018. The agricultural NUE for the Yangtze Plain significantly decreased from 50 % in 1979 to 25 % in 2018, with the largest decline of NUE in soybean, rice, and rapeseed. Simultaneously, the leached nitrogen from cropland and natural land increased, with annual rates of 4.5 and 0.22 kg N ha−1 yr−2, respectively, leading to an overall increase of nitrogen inputs to the 50 large lakes. We further examined the correlations between terrestrial nutrient sources (i.e., the leached nitrogen, total phosphorus sources, and industrial wastewater discharge) and the satellite-observed probability of eutrophication occurrence (PEO) at an annual scale and showed that PEO was positively correlated with the changes in terrestrial nutrient sources for most lakes. Agricultural nitrogen and phosphorus sources were found to explain the PEO trends in lakes in the western and central part of the Yangtze Plain, and industrial wastewater discharge was associated with the PEO trends in eastern lakes. Our results revealed the importance of terrestrial nutrient sources for long-term changes in eutrophic status over the 50 lakes of the Yangtze Plain. This calls for region-specific sustainable nutrient management (i.e., nitrogen and phosphorus applications in agriculture and industry) to improve the water quality of lake ecosystems.