Phytoplankton density can be influenced by a wide range of factors whereas the role of suspended particulate matter (SPM) are not clear in river that annually subjected to hydrodynamics shift. Here, spatial-temporal variation of environmental parameters and phytoplankton density were studied from January 2013 to December 2014 in Yulin River, a tributary of the Three Gorges Reservoir, China. Laboratory experiments were conducted to elucidate the key parameter and interpret how it impacted phytoplankton density. SPM is negatively correlated with phytoplankton density. Despite SPM in Yulin River revealed weaker NH3-N, NO3-N and PO4-P adsorption capabilities in comparison to that in other aquatic ecosystems, increase of water velocity from 0.1 to 0.8 m/s led to approximately 6.8-times increase of light attenuation rate. In experiments evaluating the aggregation of Chlorella pyrenoidosa upon SPM, floc size showed 7.4 to 22% fold increase compared to the SPM or algae itself, which was due to the interaction between SPM and phytoplankton extracellular polymeric substances. Our results suggest that SPM could contribute to the variation of phytoplankton density through the integrated process including light attenuation, nutrient adsorption and algae aggregation. This is the first evaluation of the multiple processes underlying the impact of SPM on phytoplankton.