In order to evaluate the environmental impacts associated with the presence of low-level of pharmaceuticals in waters, chronic ecotoxicity of carbamazepine (CBZ), oxcarbazepine (OxCBZ) and acridine 9-carboxylic acid (9-CAA) and their mixture was investigated using two species from different trophic levels. Innovative approaches were developed by monitoring: (i) phytometabolites in the duckweed Lemna minor L. and, (ii) alterations at the population, cellular and molecular levels on the cnidarian Hydra circumcincta Schulze 1914, to assess the effects of 14-day chronic exposure. On H. circumcincta, the approach was conducted at 19.5 °C, the optimal growth temperature, and at 23 °C, to simulate global warming impact. In L. minor, results showed alterations of the nitrogen balance and the chlorophyll indices for OxCBZ and 9-CAA separately at environmental concentrations and for the mixture of the three studied products. However, phenolic compound index deeply varied depending on pharmaceuticals and time of exposure with no specific trend. In H. circumcincta, effects on morphology, reproduction and lipid peroxidation were observed at low level of CBZ. OxCBZ impacted the total antioxidant capacity of H. circumcincta, whereas exposure to 9-CAA affected all parameters, except the reproduction rate. Finally, 14-day exposure to the mixture of the three products also slowed the reproduction rate and altered the morphology of this cnidarian. Higher damages were detected when experiments were conducted at a temperature 3.5 °C above the optimum for Hydra growth, suggesting the relevance of taking into account possible ecotoxicological consequences of global warming. Our results confirmed the necessity of selecting sensitive organisms at different trophic levels to better assess ecotoxicity of pharmaceuticals and their mixture, especially at environmental levels and facing global changes.