Infaunal invertebrates are affected by the overlying water and the sediment in which they live. Therefore, understanding how these environmental conditions impact infauna is critical for evaluating how they may respond to future changes in these conditions due to climate change. Here, we considered which abiotic variables, for example, salinity, sediment characteristics (i.e. mean grain size, sorting), and water column and sediment carbonate chemistry, influence infaunal invertebrate communities and juvenile bivalve abundance at intertidal sites. We used data from sites in two regions in New Brunswick, Canada with contrasting tidal regimes and oceanographic conditions, the Bay of Fundy and the Southern Gulf of St. Lawrence. We were particularly interested in bivalve recruitment due to the importance of bivalves in ecosystem services and predicted sensitivity to climate change impacts. Using data collected in 2020 and 2021, statistical modeling was done to determine which abiotic variables were potential drivers of multivariate community composition as well as species richness, total abundance, and juvenile bivalve abundance. We found that carbonate chemistry variables, both sediment and water, explained a large amount of variation (~ 7–44%) in infaunal invertebrate communities in the two regions in both our multivariate and univariate analyses. Sediment pH explained the most variation (16.9%) in the multivariate analyses for the Bay of Fundy sites. However, in the Southern Gulf of St. Lawrence, salinity explained the most variation (9.8%) in the multivariate community composition. In the univariate modeling, alkalinity, either water column or sediment, was included in all top models for all four dependent variables, suggesting the importance of this carbonate chemistry variable for bivalves and infaunal communities. Climate change is expected to have large impacts on carbonate chemistry conditions in the oceans, specifically pH, carbonate availability, and alkalinity. The influence of carbonate chemistry parameters on infaunal invertebrate communities in these regions shows the potential sensitivity these animals have to future oceanic conditions.