Chlorophyll-a (Chl-a) and algal cell density (ACD) are vital for assessing algal proliferation and eutrophication in aquatic ecosystems. Although Chl-a is often used as a proxy for ACD, its accuracy requires validation, and studies on their linear correlation are scarce. Additionally, Chl-a and ACD are influenced by various factors, including nutritional, economic, biochemical, physicochemical, and meteorological factors. However, the relative importance of these factors on Chl-a and ACD remains insufficiently studied. This study analyzed data from 57 lakes and reservoirs across China from March 2021 to February 2023, investigating the distribution patterns of Chl-a and ACD across different regions and seasons. The study employed a linear regression model to explore the correlation between Chl-a and ACD in various regions and seasons throughout China. Furthermore, Mantel test and generalized linear model were used to evaluated the relative importance of nutritional factors (total nitrogen (TN), total phosphorus (TP), TN/TP ratio (TN/TP), and ammonia nitrogen (NH3-N)), economic factors (gross domestic product), meteorological factors (surface pressure, net solar radiation, air temperature, wind speed (WS), and rainfall (RF)), as well as biochemical and physicochemical factors (turbidity (TUR), pH value, water temperature (WT), permanganate index, and dissolved oxygen) on Chl-a and ACD. Results showed that the average concentrations of Chl-a and ACD in South China were highest, at 12 μg/L and 19.5 × 106 cells/L, respectively. Seasonally, Chl-a peaked in spring and was lowest in winter, while ACD peaked in summer and was lowest in winter. Significant seasonal and regional variations in the Chl-a and ACD correlation were observed, with spring showing the strongest relationship. In Central China, Chl-a and ACD were significantly correlated throughout the four seasons, whereas correlations were less distinct in Eastern and Western regions. Therefore, Chl-a as a proxy for ACD requires caution. Nutrient factors (TN, TP, TN/TP, NH3-N) were identified as the primary drivers of Chl-a and ACD. Meteorological factors (WS, RF), along with biochemical and physicochemical factors (WT, TUR) also emerged as critical predictors of Chl-a and ACD, with spatial variations. This study validates Chl-a as a proxy for ACD, analyzes their spatiotemporal distribution, and assesses the influence of various factors on Chl-a and ACD, enhancing our understanding of algal dynamics in Chinese lakes and reservoirs.