Spatial variations in summertime phytoplankton community structure from 1991 to 2017 in Daya Bay, China were investigated in this research. The abundance of total phytoplankton and diatoms significantly increased during the study period in all regions of the bay while an increase in dinoflagellates abundance was only significant in the inner and middle bay areas. Pseudo-nitzschia spp. were overwhelmingly dominant followed by Skeletonema costatum. Ceratium furca was the dominant dinoflagellate. Overall, species diversity and evenness indices showed downward trends during the study period. Moreover, the bloom frequency of Scrippsiella trochoidea (associated with red tides) has increased rapidly since the 2000s in the inner bay. These temporal dynamics are largely explained by enhanced dissolved inorganic nitrogen (DIN) concentrations, which increased by 64.58% during 2005–2017 relative to 1991–2004, induced by human activities, along with temperature reductions and salinity increases resulting from open oceanic seawater intrusion.