Unprecedented levels of chemicals of anthropogenic origin are currently released into surface waters globally. Wastewater treatment plant effluent has been identified as a major source, containing a broad mixture of pharmaceuticals and consumer chemicals. Therefore, there is a need for implementation of advanced wastewater treatment techniques, such as ozonation and adsorption methods, to reduce the contamination. However, there are conflicting findings on the toxicity of treated effluent and only limited possibilities for assessing the effect-based removal efficiency (EBRE) of different treatment techniques. Here, we describe a metabolomics approach to detect perturbations in fatty acid catabolic pathways as a proxy for biological effects. Metabolites in three fatty acid pathways were analyzed in a common damselfly larva (Coenagrion hastulatum) by liquid chromatography coupled to mass spectrometry. The larvae were exposed for one week to either conventionally treated effluent (activated sludge treatment), effluent additionally treated with ozone or effluent additionally treated with biochar filtration and results were compared with those from tap water control exposure. Five lipoxygenase-derived oxylipins (9,10,13-TriHOME, 9,12,13-TriHOME, 9-HODE, 9-HOTrE, and 13-HOTrE) decreased in response to conventionally treated effluent exposure. By using an additional treatment step, oxylipin levels were restored with exception of 9,10,13-TriHOME (ozonated effluent), and 9-HOTrE and 13-HOTrE (effluent filtered with biochar). In conclusion, exposure to wastewater effluent affected fatty acid metabolite levels in damselfly larvae, and a subset of the analyzed metabolites may serve as indicators for biological effects in biota in response to effluent exposure. To that effect, our findings suggest a new metabolomics protocol for assessing EBRE.