Fecal indicator bacteria (FIB) are leading causes of impaired surface waters. Innovative and environmentally appropriate best management practices are needed to reduce FIB concentrations and associated risk. This study examines the ability of the native freshwater mussel Anodonta californiensis and an invasive freshwater clam Corbicula fluminea to reduce concentrations of the FIB Escherichia coli in natural waters. Laboratory batch experiments were used to show bivalve species-specific E. coli removal capabilities and to develop a relationship between bivalve size and clearance rates. A field survey within an impaired coastal river containing both species of bivalves in an agricultural- and grazing-dominated area of the central coast of California showed a significant inverse correlation between E. coli concentration and bivalve density. An in situ field spiking and sampling study showed filtration by freshwater bivalves resulting in 1-1.5 log10 reduction of E. coli over 24 h, and calculated clearance rates ranged from 1.2 to 7.4 L hr-1 bivalve-1. Results of this study show the importance of freshwater bivalves for improving water quality through the removal of E. coli. While both native and invasive bivalves can reduce E. coli levels, the use of native bivalves through integration into best management practices is recommended as a way to improve water quality and protect and encourage re-establishment of native bivalve species that are in decline.