Freshwater mussels (Bivalvia: Unionidae) are sensitive to pollution of stream habitats. However, there has been no analysis of whether mussel density is correlated with measurements from commonly used rapid water assessment protocols. This study tested which water quality parameters are correlated with the density of freshwater mussels found in selected locations of the middle Allegheny River, PA. No correlation was found between mussel density and either temperature or chemical water quality parameters. However, there was a strong positive correlation between mussel density and the modified EPA physical habitat parameters tested. These results suggest that the physical habitat variables are a useful tool to assess the suitability of stream habitat for unionid mussels, and should help ecosystem managers make informed decisions about the maintenance or restoration of the ecosystem function that these mussels perform.