Development of effective conservation and restoration strategies for freshwater pearly mussels requires identification of environmental constraints on the distributions of individual mussel species. We examined whether the spatial distribution of the endangered Alasmidonta heterodon in Flat Brook, a tributary of the upper Delaware River, was constrained by water chemistry (i.e., calcium availability), bed mobility, or both. Alasmidonta heterodon populations were bracketed between upstream reaches that were under-saturated with respect to aragonite and downstream reaches that were saturated for aragonite during summer baseflow but had steep channels with high bed mobility. Variability in bed mobility and water chemistry along the length of Flat Brook create a “habitat window” for A. heterodon defined by bed stability (mobility index ≤1) and aragonite saturation (saturation index ≥1). We suggest the species may exist in a narrow biogeochemical window that is seasonally near saturation. Alasmidonta heterodon populations may be susceptible to climate change or anthropogenic disturbances that increase discharge, decrease groundwater inflow or chemistry, and thus affect either bed mobility or aragonite saturation. Identifying the biogeochemical microhabitats and requirements of individual mussel species and incorporating this knowledge into management decisions should enhance the conservation and restoration of endangered mussel species.