Adverse habitat conditions associated with reduced seawater pH often, but not always, negatively affect bivalves in early life history phases. Improving our understanding of how habitat-specific parameters affect clam recruitment, survival, and growth could assist natural resource managers and researchers in developing appropriate adaptation strategies for increasingly acidified nearshore ecosystems. Two proposed adaptation strategies, the presence of macrophytes and addition of shell hash, have the potential to raise local seawater pH and aragonite saturation state and, therefore, to improve conditions for shell-forming organisms. This field study examined the effects of these two substrate treatments on biological and geochemical response variables. Specifically, we measured (1) recruitment, survival, and growth of juvenile clams (Ruditapes philippinarum) and (2) local water chemistry at Fidalgo Bay and Skokomish Delta, Washington, USA, in response to experimental manipulations. Results showed no effect of macrophyte or shell hash treatment on recruitment or survival of R. philippinarum. Contrary to expectations, clam growth was significantly greater in the absence of macrophytes, regardless of the presence or absence of shell hash. Water column pH was higher outside the macrophyte bed than inside at Skokomish Delta and higher during the day than at night at Fidalgo Bay. Additionally, pore-water pH and aragonite saturation state were higher in the absence of macrophytes and the presence of shell. Based on these results, we propose that with increasingly corrosive conditions shell hash may help provide chemical refugia under future ocean conditions. Thus, we suggest adaptation strategies target the use of shell hash and avoidance of macrophytes to improve carbonate chemistry conditions and promote clam recruitment, survival, and growth.