This study investigated phytoplankton and bacterioplankton communities by flow cytometer in a tributary backwater area of the Three Gorges Reservoir, China. Samplings were conducted in two cyanobacterial bloom periods (May and August) and no algal-blooms period (November) of 2014, representing three different operational stages of the reservoir, i.e., reservoir discharge period, fluctuating period in the summer flood season, and high water level in the impoundment period. Phyto- and bacterioplankton exhibit a wide range of variability along the depth profiles of the water column. In the investigated two cyanobacterial bloom periods, prokaryotes accounted for over 50% of the total phytoplankton. As for bacterioplankton, low nucleic acid bacteria were dominant in August and November. A positive correlation was observed between phytoplankton (pico- and nanophytoplankton), Chl a, and bacterioplankton. High nucleic acid groups and prokaryotes were highly coupled in May and August, which indicated that this high nucleic acid group could probably contribute to the explanation of cyanobacterial bloom formation in this area.