The aim of this study was to determine the spatial and temporal variation of phytoplankton and water quality in response to the hydrological regime in an isolated floodplain lake (North Mollaköy Lake) of the Sakarya River. Variations in the composition, biomass and functional groups of phytoplankton and environmental parameters were monthly analyzed in subsurface samples collected from the pelagic zone at four stations from July 2012 to June 2013. A total of 109 taxa were identified, and the species which contributed the most to the phytoplankton biomass were grouped into 14 functional groups (FGs). The distribution of FGs was linked to the transition (T1 and T2), high (HW) and low (LW) water periods in North Mollaköy Lake. FGs J, MP, N, G, X1, X2, Y, W1, W2, S1, H1, B and C were the contributors to the phytoplankton biomass during the low-water period (LW) and the transition periods (T1 and T2), while Lo contributed the most during the high-water period (HW). RDA revealed that the most important factor affecting the temporal distribution of FGs was the water discharge and that there are