This paper describes the mathematical model used to compute the filtration and assimilation rates of two filter-feeding bivalves, Venus verrucosa and Mytilus galloprovincialis fed on the enteric bacteria Escherichia coli. The model initially consisted of six compartments: bivalves, bacteria, dissolved organic matter (DOM), CO2, biodeposits, and resuspended biodeposits. We introduced three second-order time-delays to account for the time lags between ingestion of radioactive materials and (1) the production of radioactive biodeposits, (2) the production of radioactive DOM, and (3) the production of radioactive CO2 by the bivalves. These delays resulted in the subdivision of the bivalves compartment into three subcompartments: Bivalves 1, Bivalves 2, Bivalves 3. The model simulates the exchanges of radioactivity between compartments, and allows the quantification of the radioactivity corresponding to compartments that cannot be directly measured (i.e., bacteria and biodeposits). Our results show that M. galloprovincialis ingests E. coli more quickly than does V. verrucosa (kinetic coefficients of 0.280 and 0.120, respectively). Neither bivalve seems able to efficiently assimilate E. coli. The assimilation rates of V. verrucosa and M. galloprovincialis are between 11.1 and 20.4%, and 7.5 and 14.8%, respectively. Because of the low assimilation rates recorded during this study, because of the resuspension of the biodeposits produced, and because of the presence of culturable E. coli in biodeposits of both bivalves, our conclusions are that: (1) filter-feeding bivalves are probably inefficient in purifying seawater polluted by the tested strain of E. coli, and (2) as opposed to marine bacteria and other previously tested enteric bacteria, the strain of E. coli used during the present study probably does not constitute a suitable food source for filter-feeding bivalves.