Algae are important primary producers in lake ecosystems, with high species diversity and sensitivity to changes in water environment. Algal productivity and community structure can serve as reliable indicators for tracking the lake environmental gradient and ecosystem features. The succession of dominant diatom species and the identification of environmental gradients are important in evaluating lake ecological health and environmental quality. In order to quantify the spatio-temporal variations in lake-water chlorophyll-a (Chi.a) and diatom communities, a seasonal survey of diatom composition and limnological characteristics was carried out at 20 sampling sites of Lake Yilong for assessing the driving factors of algal distribution and the degree of similarity between both indicators. From December 2020 to September 2021, the water environment displayed strongly seasonal fluctuations, and the trophic state index (TSI) varied with a mean of 74.76, suggesting the persistence of a eutrophie level across seasons. A total of 68 diatoms species belonging to 21 genera were identified in 80 water samples, mainly comprising planktonic species (relative abundance, mean±SD; 79.33% ±20.69%). Specifically, Aulacoseira ambigua (61.62% ±20.26%) was found to be the dominant species across seasons. Principal components analysis (PCA) showed that there were significant spatial heterogeneity and seasonal variations in diatom communities. The results of redundancy analysis and variance partitioning showed that nutrient variables (e.g., TN, TP and N -P) were the important factors causing spatial variation of lake-water chlorophyll-a concentration (an explained variance of 19.08%i ± 11.4%), while the gradients of water temperature and depth played a secondary and moderate role (9.63% ±11.31%). Similarly, nutrition variables (e.g., TN, TP, N:P and Si03~) were identified as key factors in structuring diatom communities, accounting for 27.55% ± 15.83% of the community variances. While water temperature and depth were insignificant in influencing the spatial variation of diatom community structure (2.53% ±3.78%i), however, their interaction with nutrient level played a much stronger role (15.95% ± 11.45%). The results of multiple regression analysis further showed that water temperature had predominant impacts on the seasonal variation in both algae biomass and diatom community distribution (56.4% and 20.1%), while the role of nutrient factors (TN, TP, N:P and Si03~ etc.) was relatively small (6.5%> and 19.2%). In conclusion, the nutrient served as a key factor in causing spatial heterogeneity of algal distribution, while water temperature was an important driver of seasonal changes in phytoplankton in Lake Yilong. Meanwhile, there existed significant differences in the driving processes for seasonal and spatial distribution of lake-water algae as indicated by diatom community structure and primary productivity. This study provides empirical evidence on the strongly seasonal fluctuation and spatial heterogeneity in the limnological properly and ecological processes in subtropical shallow lakes, and implies that it is imperative to combine multiple indicators of algae for an integrated assessment of lake environment quality and ecological health. © 2023 Science Press. All rights reserved.