Lake eutrophication is influenced by both anthropogenic and natural factors. Few studies have examined relationships between eutrophication parameters and natural factors at a large spatial scale. This study explored these relationships using data from 103 lakes across China. Eutrophication parameters including total nitrogen (TN), total phosphorus (TP), TN:TP ratio, chemical oxygen demand (COD_Mn), chlorophyll-a (Chl-a), Secchi depth (SD), and trophic state index (TSI) were collected for the period 2001–2005. Sixteen natural factors included three of geographic location, five of lake morphology, and eight of climate variables. Pearson correlation analysis showed that TP and TSI were negatively related to elevation, lake depth, and lake volume, and positively related to longitude. All eutrophication parameters, except for COD_Mn and Chl-a, showed no significant correlation with climate variables. Multiple regression analyses indicated that natural factors together accounted for 13–58% of the variance in eutrophication parameters. When the 103 study lakes were classified into different groups based on longitude and elevation, regression analyses demonstrated that natural factors explained more variance in TN, TP, COD_Mn, Chl-a, and TSI in western lakes than in eastern lakes. Lake depth, volume, elevation, and mean annual precipitation were the main predictors of eutrophication parameters for different lake groups. Although anthropogenic impacts such as point- and nonpoint-source pollution are considered as the main determinants of lake eutrophication, our results suggest that some natural factors that reflect lake buffer capacity to nutrient inputs can also play important roles in explaining the eutrophication status of Chinese lakes.