Since it has been demonstrated that urban effluents can have adverse effects on aquatic organisms, a multibiomarker study was used to evaluate the effects of wastewater treatment plant (WWTP) effluents discharged into the marine and freshwater environments on clams in Cádiz, Spain. One bioassay was performed in the Bay of Cádiz, exposing Ruditapes philippinarum (marine) to a reference site as well as two sites close to WWTP discharges for 14 days. A second bioassay was performed in the Guadalete River, exposing Corbicula fluminea (fresh water) to three sites for 21 days. The biomarkers analysed included defence mechanisms and various toxic effects. Results indicated that WWTP effluents activated defence mechanisms and induced toxic effects in clams exposed to both environments, thus indicating bioavailability of contaminants present in water. Elevated enzymatic activity was found in clams deployed in La Puntilla and El Trocadero compared to control clams and those exposed to the reference site, and 96% of clams deployed at G2 in the Guadalete River died before day 7. Clams exposed to G1 and G3 indicated significant differences in all biomarkers analysed with respect to control clams (p < 0.05). Both species were sensitive to contaminants present in studied sites. This is the first time that these species were used in cages to assess the environmental risk of wastewater effluent discharges in freshwater and marine column environments. The multibiomarker approach provided important ecotoxicological information and is useful for the assessment of the bioavailability and effect of contaminants from WWTP effluents on marine and fresh water invertebrates.