Effects of anthropogenic activities such as urbanisation, population growth and agriculture on water quality are major concerns particularly in low-income countries where water quality monitoring can be challenging. The purpose of this study was to evaluate the cytogenotoxic potential of water from urban and rural Malagasy marshes, coupling a fish (Nile tilapia Oreochromis niloticus) and a plant (Allium cepa) species as bioindicators. The fish and plants were exposed for 72 h to water sampled in the two locations investigated. DNA strand breaks were assessed using the comet assay on fish erythrocytes, while mitotic index and nucleolar alterations were estimated in cells of the plant root apex. Comet assays revealed significant DNA strand breaks to fish erythrocytes in both the marshes investigated while the mitotic index and nucleolar characteristics in the roots of A. cepa mainly highlighted potential cytotoxicity in the urban marsh. Our results demonstrate the advantages of coupling in vivo biological test systems to screen potential cytogenotoxicity of surface water in low-income countries where comprehensive datasets of aquatic contaminants are often lacking. This article is protected by copyright. All rights reserved. Environ Toxicol Chem 2023;00:0-0. (c) 2023 SETAC.