Excessively used pesticides in agricultural areas are spilled into aquatic environments, wherein they are suspended or sedimented. Owing to climate change, herbicides are the fastest growing sector of the pesticide industry and are detected in surface water, groundwater, and sediments near agricultural areas. In freshwater, organisms, including mussels, snails, frogs, and fish, are exposed to various types and concentrations of herbicides. Invertebrates are sensitive to herbicide exposure because their defense systems are incomplete. At the top of the food chain in freshwater ecosystems, fish show high bioaccumulation of herbicides. Herbicide exposure causes reproductive toxicity and population declines in freshwater organisms and further contamination of fish used for consumption poses a risk to human health. In addition, it is important to understand how environmental factors are physiologically processed and assess their impacts on reproductive parameters, such as gonadosomatic index and steroid hormone levels. Zebrafish is a good model for examining the effects of herbicides such as atrazine and glyphosate on embryonic development in freshwater fish. This review describes the occurrence and role of herbicides in freshwater environments and their potential implications for the reproduction and embryonic development of freshwater organisms.