Bacteria are ingested by suspension feeding bivalves and can be an important component of their diet. This study evaluated whether a common bacterium of vertebrate enteric origin, Escherichia coli (Migula, 1895), is retained in the stomach or gill by two different freshwater bivalve species, Corbicula fluminea (Müller, 1974) and Elliptio complanata (Lightfoot, 1786). A series of diet treatment experiments were conducted comparing each anatomical section using a δ¹³C label and E. coli cells grown from stock cultures. A significant difference in δ¹³C values was related to anatomic structure among all treatment groups during a 7-day feeding experiment (24 jars, df = 140; F = 4.88; P < 0.001). A key finding was that in gill tissue, a significant difference was observed among <δ¹³C-labeled and unlabeled treatment combinations for both C. fluminea and E. complanata (F = 13.57; df = 31; P < 0.0001). The results suggest that water column E. coli are likely retained on gill tissue and to a lesser degree in the stomach in both E. complanata and C. fluminea. This study serves to validate the hypothesis that E. coli may be initially more abundant in gill tissue during sorting processes before being transferred to the stomach.