A global evaluation of wastewaters should include ecotoxicological tests to complement the chemical characterization, with advantages especially in the case of complex wastewaters. A European project developed in Trancão River Basin (Portugal), integrated the ecotoxicological and physicochemical studies of wastewater samples from two municipal sewer networks and respective wastewater treatment plants. Wastewater samples were analysed for physicochemical parameters, ecotoxicological acute and chronic tests performed and the potential for endocrine disruption evaluated. Organic load parameters and total suspended solids showed significant correlations with Microtox and ThamnoToxKit test results. Data analysis showed that treated treatment plant effluent samples are associated with less organic contamination and less toxicity in ThamnoToxKit test. Chronic toxicity test and endocrine disruption assay of treatment plant effluent samples indicated that, in a long term, potential population effects could arise in the receiving waters. A test battery to monitor this type of wastewaters is proposed, including tests with a bacterium, an alga and a crustacean. In a screening phase the most sensitive test, Microtox, can be used. The use of an ecotoxicological approach can have added value to hazard and risk assessment of discharges to the receiving waters and can contribute to the environmental management of the treatment plant.