The present review addresses the impacts of pesticides used in crops on non-target organisms in aquatic ecosystems. In recent decades, these ecosystems have received large amounts of these compounds, which are released by urban communities, rural and industrial properties. Pesticides reach the aquatic environment through different routes (leaching, irrigation, drainage, and surface runoff) and can easily reach non-target organisms, such as fish, mollusks, as well as other benthic organisms. Usually, these animals tend to undergo bioaccumulation. Exposure to these pesticides can cause numerous physiological changes by direct influence on certain cellular structures, such as on the lysosomal membrane, which can be degraded. Also, they can even react with nucleic acids resulting in several genetic injuries, thus causing adverse reactions to the body. There is a need for more incentives for the adoption of sustainable agroecological practices, as well as a ban on active ingredients harmful to the environment, in addition to strict inspection by competent environmental agencies.