The effects of pharmaceuticals on aquatic ecosystems are the subject of increasing environmental concern. Of particular interest are a suite of drugs known as selective serotonin reuptake inhibitors (SSRIs), commonly prescribed to treat depression. SSRIs are now detected in the environment worldwide, but their effects on ecosystems are not well understood. We conducted replicated experiments testing for an ecosystem effect of SSRIs in streams. We used artificial stream mesocosms to expose natural biofilms and aquatic insect communities to concentrations (20 µg/L) of fluoxetine or citalopram or a mix of both (totaling 40 µg/L). These concentrations are the lowest found to have an effect on aquatic invertebrates in other studies. Treatments suppressed gross primary production by 29% and community respiration by >43% on rock biofilms but did not affect algal biomass or whole-stream metabolism. A common group of dipteran midges emerged earlier in all SSRI treated streams compared with the controls. Total biomass of emerged adults at day 14 was greater in the SSRI-exposed streams, suggesting that fluoxetine and citalopram may influence developmental processes in some stream insects. Ecosystem function and invertebrate population dynamics are sensitive to pharmaceuticals. Our study demonstrates that chronic exposure to fluoxetine and citalopram has the potential to affect aquatic biota and ecosystem function.