Although ocean acidification is expected to reduce carbonate saturation and yield negative impacts on open-ocean calcifying organisms in the near future, acidification in coastal ecosystems may already be affecting these organisms. Few studies have addressed the effects of sedimentary saturation state on benthic invertebrates. Here, we investigate whether sedimentary aragonite saturation (Ω_aragonite) and proton concentration ([H⁺]) affect burrowing and dispersal rates of juvenile soft-shell clams (Mya arenaria) in a laboratory flume experiment. Two size classes of juvenile clams (0.5–1.5 mm and 1.51–2.5 mm) were subjected to a range of sediment Ω_aragonite and [H⁺] conditions within the range of typical estuarine sediments (Ω_aragonite 0.21–1.87; pH 6.8–7.8; [H⁺] 1.58 × 10^− 8–1.51 × 10^- 7) by the addition of varying amounts of CO₂, while overlying water pH was kept constant ~ 7.8 (Ω_aragonite ~ 1.97). There was a significant positive relationship between the percent of juvenile clams burrowed in still water and Ω_aragonite and a significant negative relationship between burrowing and [H⁺]. Clams were subsequently exposed to one of two different flow conditions (flume; 11 cm s^− 1 and 23 cm s^− 1) and there was a significant negative relationship between Ω_aragonite and dispersal, regardless of clam size class and flow speed. No apparent relationship was evident between dispersal and [H⁺]. The results of this study suggest that sediment acidification may play an important role in soft-shell clam recruitment and dispersal. When assessing the impacts of open-ocean and coastal acidification on infaunal organisms, future studies should address the effects of sediment acidification to adequately understand how calcifying organisms may be affected by shifting pH conditions.