Healthy plankton communities form the basis of healthy aquatic ecosystems. By elucidating the mechanisms of mutual feedback between plankton and habitat processes and identifying key driving factors can enhance the success rate of ecosystem restoration. However, previous studies suffered from a lack of consideration for temporal and spatial variation in aquatic biome. In this study, three sets of samples were collected in May, September and October 2015 from 59 sampling sites in Jinan, a pilot city for water ecological civilization project, China. Canonical correspondence analysis was performed on the vast amount of data obtained from the samples to analyse the driving effects of various hydrological and water quality factors on plankton. The analysis results indicated that the development of plankton communities in Jinan were primarily driven by (1) hydrological factors of water depth, river width and flow velocity; (2) water quality physical factors of water temperature and conductivity and (3) water quality chemical factors of pH, chemical oxygen demand, biochemical oxygen demand, carbonate and sulphate contents. These results will provide in-depth theoretical and technical direction for the restoration of aquatic ecosystems in the first pilot city in China and other regions worldwide. K E Y W O R D S aquatic ecosystem, canonical correspondence analysis, hydrological and water quality factors, Jinan City