Sustainable aquaculture arises as key to increase food production in the coming years. However, the sector still faces many challenges such as the exposure of the cultured animals to pesticide-contaminated water. Pesticides used in agriculture can reach aquaculture systems either directly (integrated-agriculture aquaculture practices) or indirectly (soil leakage) and cause a broad range of ecotoxicological effects on cultured fish and shellfish. Here, we studied how glyphosate affects several haematological, biochemical, and immune parameters in common carp (Cyprinus carpio) fingerlings, the fourth most important cultured fish species worldwide. We also evaluated the potential of dietary supplementation with black seed (Nigella sativa, 0.25, 0.5 and 1%) to lower glyphosate-associated toxicity. Our results showed that 14-day sub-lethal exposure of common carp fingerlings to glyphosate increases oxidative stress, decreases antioxidant defences, affects several metabolic pathways, and induced immune depression. Furthermore, we showed that fish fed with N. sativa-enriched diets at 0.25, 0.5 and 1% for 60 days coped better with glyphosate exposure than control fish and displayed more stable levels of biochemical serum parameters (total protein, albumin, triglycerides, low-density lipoprotein LDL), cholesterol and high-density lipoprotein HDL), higher levels of immune defences (lysozyme and immunoglobulin) and higher antioxidant enzymes (superoxide dismutase SOD, glutathione peroxidase GPx) than control fish. Fish fed with all enriched diets also displayed lower lipid peroxidation (malondialdehyde MDA), lower metabolic enzymes (alanine aminotransferase ALT, aspartate aminotransferase AST and alkaline phosphatase ALP) levels in blood serum and lower cortisol levels than control fish. Altogether, our results show that dietary inclusion of black seed can be used as a sustainable bio-remediation strategy, mitigating many of the negative effects of glyphosate exposure in fish. © 2020 Elsevier Ltd