Population dynamics in the microbial food web are influenced by resource availability and predator/parasitism activities. Climatic changes, such as an increase in temperature and/or UV radiation, can also modify ecological systems in many ways. A series of enclosure experiments was conducted using natural microbial communities from a Mediterranean lagoon to assess the response of microbial communities to top‐down control [grazing by heterotrophic nanoflagellates (HNF), viral lysis] and bottom‐up control (nutrients) under various simulated climatic conditions (temperature and UV‐B radiations). Different biological assemblages were obtained by separating bacteria and viruses from HNF by size fractionation which were then incubated in whirl‐Pak bags exposed to an increase of 3°C and 20% UV‐B above the control conditions for 96 h. The assemblages were also provided with an inorganic and organic nutrient supply. The data show (i) a clear nutrient limitation of bacterial growth under all simulated climatic conditions in the absence of HNF, (ii) a great impact of HNF grazing on bacteria irrespective of the nutrient conditions and the simulated climatic conditions, (iii) a significant decrease in burst size (BS) (number of intracellular lytic viruses per bacterium) and a significant increase of VBR (virus to bacterium ratio) in the presence of HNF, and (iv) a much larger temperature effect than UV‐B radiation effect on the bacterial dynamics. These results show that top‐down factors, essentially HNF grazing, control the dynamics of the lagoon bacterioplankton assemblage and that short‐term simulated climate changes are only a secondary effect controlling microbial processes.