Lakes are vital sources of drinking water and essential habitats for humans and various other living organisms. However, many lakes face organic pollution due to anthropogenic disturbance and climatic influence, and the spatiotemporal changes of organic pollution in lakes over a large area are still unclear. Based on three monitoring datasets of chemical oxygen demand (COD) in 390 lakes, this study demonstrated the apparent spatiotemporal differences of organic pollution in lakes during the 1980s-2010s and the effects of water eutrophication and salinization. Throughout China, lake organic pollution showed a general spatial trend of being more severe in the north compared to the south. This pattern is reflected in the positive linear correlations between in-situ COD concentrations and lake latitude, observed in both the 1980s (p < 0.05) and the 2010s (p < 0.01). In terms of spatial differences, the influence of total nitrogen concentrations increased from 0.27% in the 1980s to 35.24% in the 2010s. Moreover, with increasing human activity, 78.31% of the studied lakes (N = 83) showed increasing COD concentrations during the 1980s-2010s. In addition, the logarithmic dissolved organic carbon concentrations were linearly correlated with log water conductivities (Pearson's r = 0.49, p < 0.01), suggesting that lake expansion would attenuate organic pollution in saline lakes through dilution effects. These results are valuable for understanding the spatiotemporal dynamics of organic pollution and are crucial for effective management of organic pollution in different lakes.