This study investigated the impact of four environmental factors on the recruitment of cyanobacteria from bottom sediments in the eutrophic Shanzi Reservoir. Temperature and light were identified as the key determinants for the recruitment of Microcystis and Oscillatoria. Cyanobacteria became dominant at higher temperature (20°C) and light intensity (2000 lx) and Microcystis and Oscillatoria were the major species. Detailed recruitment simulation undertaken with the respective gradients of temperature and light suggested that both Microcystis and Oscillatoria are temperature sensitive and that their critical temperature point was 10°C. However, distinct light impacts were observed only on Microcystis. The recruitment of Oscillatoria was light independent, whereas Microcystis had a positive relationship with light intensity. Physical disturbance promoted Microcystis recruitment and also affected the structure of the recruited cyanobacterial community at the water–sediment interface, based on quantitative polymerase chain reaction (qPCR) and phylogenetic analysis.