The aim of this research was to compare the phytoplankton structure on the basis of environmental variables and test the Q assemblage index based on phytoplankton functional groups in two shallow Mediterranean lakes [Lake Taşkısığı (LT) and Lake Little Akgöl (LLA)] in the north of Turkey. Variations in the phytoplankton structure and environmental parameters were analyzed monthly at two stations of each lake between January 2013 and December 2013. We showed that total phosphorus (TP) values were vital in shaping phytoplankton biomass in eutrophic LLA. Nitrate-nitrogen (NO3-N), TP, zmix/zeu, and macrophyte coverage are important in shaping the differences in dominant phytoplankton functional groups between two lakes. Generally, diversity values were similar between the two lakes and environmental parameters had no effect on diversities to constitute significant differences. The assessment using the Q index gave compatible results for determining the ecological status of LT and LLA.