Ocean acidification (OA) is one of the most significant threats to marine life, and is predicted to drive important changes in marine communities. Although OA impacts will be the sum of direct effects mediated by alterations of physiological rates and indirect effects mediated by shifts in species interactions and biogenic habitat provision, direct and indirect effects are rarely considered together for any given species. Here, we assess the potential direct and indirect effects of OA on a ubiquitous group of crustaceans: caprellid amphipods (Caprella laeviuscula and Caprella mutica). Direct physiological effects were assessed by measuring caprellid heart rate in response to acidification in the laboratory. Indirect effects were explored by quantifying caprellid habitat dependence on the hydroid Obelia dichotoma, which has been shown to be less abundant under experimental acidification. We found that OA resulted in elevated caprellid heart rates, suggestive of increased metabolic demand. We also found a strong, positive association between caprellid population size and the availability of OA-vulnerable O. dichotoma, suggesting that future losses of biogenic habitat may be an important indirect effect of OA on caprellids. For species such as caprellid amphipods, which have strong associations with biogenic habitat, a consideration of only direct or indirect effects could potentially misestimate the full impact of ocean acidification.