Ecosystem impacts of ocean acidification (OA) were explored by imposing scenarios designed to mimic OA on a food web model of Puget Sound, a large estuary in northwestern USA. The productivity of functional groups containing mostly calcifiers was decreased while still allowing other species groups to respond to the scenarios in a dynamic way through indirect effects. Results focus on changes in ecosystem services and structure. Sometimes the direct and indirect effects of OA countered each other due to interactions between predators and prey within the food web, leading to little change in the food web. In other cases, direct and indirect effects caused greater change in the food web than anticipated from direct effects alone. Results were strongly affected by the group on which OA was directly imposed, with changes in copepod productivity being the most influential. While there is much uncertainty in our predictions, focusing on the complex interactions among species, and between species and their environment, will yield better understanding of how ecosystems may respond to OA.