This study examined the main filtration variables [filtration rate (FR), clearance rate (CR) and assimilation efficiency (AE)] of the Cortez oyster, Crassostrea corteziensis (Hertlein, 1951), and the mud cockle, Anadara tuberculosa (Sowerby, 1833), in shrimp aquaculture effluents at three different flux velocities (1.5, 3 and 4.5 L h−1) using a 36-respirometer system, each with a 0.5 L capacity. Under inverted photoperiod conditions, free variations in the environmental parameters were allowed to mimic effluent conditions during a pair of 12-h trials. The FRs for both species (0.124, 0.328 and 0.402 L h−1 for the Cortez oyster; 0.093, 0.189 and 0.345 L h−1 for the mud cockle) were relatively low as compared with those reported for similar or related species. The CRs were higher for the Cortez oyster (20.04, 52.92 and 64.70 L h−1) than for the mud cockle (10.96, 22.95 and 42.12 L h−1); in both cases, the values were in the range reported previously for the last species. The AE for both mollusks (over 92% for the Cortez oyster and over 95% for the mud cockle) was very high and greater than that found by other authors for the same or related species. The three filtration variables were better at higher effluent flux velocities. These preliminary results strongly suggest that both species are good candidates to be considered for bioremediation of aquaculture effluents.