To elucidate the specific and combined effects of bottom-up and top-down control on the microbial community in warm lakes, we sampled microbial community along with physical-chemical and biological variables and performed in situ food web experiments, in 14 Turkish shallow lakes with contrasting nutrient levels and predation pressures. Our field results revealed that differences in microbial communities correlated with differences in zooplankton community structure, temperature (increasing nutrient concentrations, change in zooplankton composition), nutrient concentrations (increasing bacteria and heterotrophic nanoflagellate abundances with increasing nitrogen concentrations and temperature) and macrophyte coverage (ciliates as potential consumers of bacteria and HNF was strongest in macrophyte-dominated lakes). Our in situ experimental study revealed that the zooplankton not only affect the biomass and composition of microbial communities but also alter the microbial structure and trophic relationships. Our results therefore indicate that both bottom-up factors and top-down effects were important for the efficiency of the carbon transfer from bacteria to higher trophic levels in the study lakes. Due to an anticipated increase in eutrophication, temperature and alteration of the classical food web with climate warming, major changes in the microbial community of lakes are, therefore, expected in a warmer future in semi-arid Mediterranean climatic regions.