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In response to climate change it is expected an increase in temperature and precipitation in subtropical regions of South America. Precipitation increases surface runoff, which leads to an increased input of nutrients and suspended solids in freshwater ecosystems, resulting in changes in turbidity and water color. We analyzed the effects of increased temperature and surface runoff (simulated by soil addition) on freshwater periphytic diatom communities through a bi-factorial (temperature: ambient and increased in 2.5 degrees C; runoff: present and absent) experiment, simulating lentic waters in mesocosms of polyethylene. Diatom species richness was reduced by increased temperature. Further, runoff reduced species richness of high-profile and motile diatoms, while the interaction between temperature and runoff explained differences in relative abundances of the high-profile and planktonic (occurring occasionally entangled in the periphyton matrix) functional groups. The low-profile group was positively affected by soil addition. Temperature and runoff also affected the composition of all functional groups (low-profile, high-profile, motile, and planktonic diatoms). These results indicated different responses of diatom functional groups to temperature increase and surface runoff, showing the importance of considering ecological differences among functional groups to evaluate the possible consequences of climate change.