The role of benthic versus planktonic algae in shaping semi-natural ciliate biofilms was studied using miniature flow cells fed by a permanent flow of natural field water from the River Rhine, Germany. Increased food availability for the ciliates was achieved either by supplementation with planktonic algae or by artificial illumination (to stimulate benthic algal growth). Manipulation of both resources significantly increased the total abundance of ciliates and caused significant shifts in the structure of the ciliate community. Supplementation with planktonic algae particularly stimulated suspension-feeding Peritrichia, whereas Choreotrichia were reduced, probably due to indirect effects such as competition or interference. Increased density of benthic algae especially stimulated surface-feeding groups (e.g. Stichotrichia, Nassophorea), causing the establishment of seasonally atypical structures in the ciliate community, as has been observed in late fall. Ciliates generally responded faster to increased resources during the summer, as compared with winter, suggesting that temperature, as well as the availability of resources, has an important role in shaping ciliate biofilms. Our results are among the first that demonstrate the different contributions of planktonic and benthic algae in shaping ciliate biofilms. Furthermore, they accentuate the need for studies with a higher ­taxonomic resolution when addressing the responses of microbial biofilms to the increased avail­ability of food.