Introduction Lakes play an important role in socioeconomic development and ecological balance in China, but their water quality has deteriorated considerably in recent decades. In this study, we investigated the spatial–temporal variations of eutrophication parameters (secchi depth, total nitrogen, total phosphorus, chemical oxygen demand, chlorophyll-a, trophic level index, and trophic state index) and their relationships with lake morphology, watershed land use, and socioeconomic factors in the Yunnan Plateau lakes. Discussion Results indicated that about 77.8% of lakes were eutrophic according to trophic state index. The plateau lakes showed spatial variations in water quality and could be classified into high-nutrient and low-nutrient groups. However, because watersheds were dominated by vegetation, all eutrophication parameters except chlorophyll-a showed no significant differences between the wet and dry seasons. Lake depth, water residence time, volume, and percentage of built-up land were significantly related to several eutrophication parameters. Agricultural land use and social–economic factors had no significant correlation with all eutrophication parameters. Stepwise regression analyses demonstrated that lake depth and water residence time accounted for 73.8% to 87.6% of the spatial variation of single water quality variables, respectively. Redundancy analyses indicated that lake morphology, watershed land use, and socioeconomic factors together explained 74.3% of the spatial variation in overall water quality. The results imply that water quality degradation in the plateau lakes may be mainly due to the domestic and industrial wastewaters. This study will improve our understanding of the determinants of lake water quality and help to design efficient strategies for controlling eutrophication in the plateau region.