The studies evaluating the impact of environmental pollution on aquatic organisms have had a growing concern in recent decades. The Ocoa River runs through Villavicencio city, receiving the wastewater produced in the city. To date studies reporting the effect and the consequences of Ocoa River pollution on aquatic organisms inhabiting this water body are unknown. Haematological and genotoxicity biomarkers were evaluated in peripheral blood of two native fish species Astyanax gr. bimaculatus and Aequidens metae during rainy and dry season at three different sites of Ocoa River called Nacimiento (site 1, before entering the city), Centauros (site 2, inside the city), Caño Seco (site 3, after the city). Also, fish from a reference site with little likelihood of contamination were sampled. Alterations such as decrease in erythrocyte count, lymphocytes, haemoglobin concentration and haematocrit percentage, and increased thrombocytes and neutrophils counts, together with nuclear abnormalities in erythrocytes such as increased frequency of micronuclei, lobed, blebbed and notched nuclei and binucleate cells were observed in fish from the site 3, followed by the site 2 in rainy season. These results shown that during rainy season, sites 2 and 3 receive domestic and industrial wastewater leading to genotoxic and haematological changes in the monitored organisms.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-1753-0) contains supplementary material, which is available to authorized users.