As many chemicals with genotoxic potential are emitted to surface water, genotoxicity tests are gaining importance which led to the development of several techniques to detect directly DNA damage. The relevance of detecting the genotoxic risks associated with water pollution was firstly perceived in the late 1970s. Since that time several tests have been developed for evaluating DNA alterations in aquatic animals. These tests rely on the premise that any changes to DNA may have long-lasting and profound consequences. Sister chromatid test, chromosome aberrations, comet assay, and micronucleus test are currently the most widely employed methods to detect DNA lesions in ecotoxicology. Chromosomal aberration and sister chromatid exchanges are time consuming, resource intensive and require proliferating cell population. Hence, Comet assay and Micronucleus test as cost effective and more sensitive test systems have now been introduced for assessing the genotoxicity of chemicals. This review presents a synthesis of the state of the art in the methodologies of comet assay and micronucleus test and their contributions in aquatic environmental research. The text explores the latest knowledge and thinking on these very important approaches for the assessment of environmental health, management, and conservation. The primary concern of the present review is the measurement of genotoxic potential in aquatic organisms under field and laboratory conditions, where effects of chemicals at different levels of biological organization can be examined.