Background: Stormwater runoff from urban areas is an alarming issue to aquatic ecosystems due to its capacity to transport a wide range of contaminants threatening aquatic organisms and compromising the ecosystem integrity. This study aims to evaluate the ecotoxicological effects of stormwater in Danio rerio embryos. Methods: Water samples were collected from three water bodies: Este river, Sousa river and Vale das flores stream. In each site, sampling took place in the upstream, stormwater outlet and downstream locations. Acute fish embryo toxicity assays were performed, evaluating survival, hatching success, and morphological alterations after 96 h in unfiltered water samples. Sub-individual parameters were also evaluated through the analysis of oxidative stress biomarkers (catalase – CAT, and glutathione S-transferases – GSTs activities, and thiobarbituric acid reactive substances – TBARS levels), neurotoxicity (acetylcholinesterase - AChE activity), and cellular energy allocation (CEA). Results: All sampling sites induced morphological abnormalities in D. rerio embryos (e.g., body curvature, hemagglutination and pericardial edema). Higher frequencies were observed in Este and Vale das Flores samples (5-25%). Sousa samples impaired embryo hatching, and caused highest mortality (>95%). Biomarkers responses varied among the studied water bodies. In the Este river, antioxidant system alterations suggest defensive mechanisms activation against oxidative damage, while changes in AChE activity indicate neurotoxic effects. Sousa samples evoked a pronounced toxic response, characterized by enhanced lipid peroxidation alongside alterations in AChE activity and CEA, indicating both oxidative damage and neurotoxicity. Vale das Flores samples caused occasional alterations in TBARS levels and CEA, nonetheless, consistent neurotoxic effects were observed. Conclusions: The results revealed distinct toxicity profiles among the urban-influenced water bodies. Sousa samples exerted the most severe effects on embryonic development. These findings highlight the sensitivity of early life stages to urban-associated stressors and reinforce the importance of incorporating ecotoxicological bioassays into monitoring strategies, improving the assessment/management of urban freshwater ecosystems.