Alterations in ocean carbonate chemistry caused by anthropogenic carbon dioxide are widely documented to adversely impact a wide range of marine taxa. Emergent pollutants, such as pharmaceuticals, are of pressing concern as they may act on non-target organisms. Nevertheless, the bioavailability and bioaccumulation of these pollutants are pH-dependent; however, the interactive effects of reduced pH and environmentally relevant concentrations of pharmaceuticals are rarely studied. Here, we exposed larvae of urchin (Heliocidaris crassispina) and ascidian (Styela plicata) to the antidepressant fluoxetine at environmentally relevant concentrations under future ocean conditions. Acidified urchin larvae swam with reduced horizontal speed and in straighter trajectories. Arm orientation was also affected by both pH and fluoxetine concentration, indicating a stronger prevalence of downward swimming in control pH and 100 ng/L fluoxetine compared to 0 and 10 ng/L. In contrast, ascidian larval behavior was only mildly affected by acidification and fluoxetine exposure, indicated by a change in relative proportion of actively swimming individuals. These observed behavioral changes take place at concentrations much lower than published lethal concentrations of fluoxetine, which have non-additive interactions with end-of-century acidification levels. Such sub-lethal impacts on behaviors can have population-level implications and highlight the need for improved pharmaceutical monitoring and control in coastal waters.