Public awareness of worldwide increase herbicides use and their adverse effects on ecosystems has been growing over the past decades. Herbicides may reach water bodies via agricultural runoff and leaching processes, as well as by direct applications to control noxious aquatic weeds. Once in the aquatic ecosystems, herbicides may reduce environmental quality and influence essential ecosystem functioning by reducing species diversity and community structures, modifying food chains, changing patterns of energy flow and nutrient cycling and changing the stability and resilience of ecosystems. The aim of this chapter is to provide a general notion of the current knowledge concerning the direct and indirect effects of glyphosate and commercial formulations of glyphosate on aquatic ecosystems. Glyphosate based products are the leading post-emergent, systemic and nonselective herbicides for the control of annual and perennial weeds in the world. Here, we present a revision of their toxicity to non-target species of algae, aquatic plants, protozoa, crustaceans, molluscs, fish and amphibians. In addition, we describe the importance of each group of organisms in the functioning and health of aquatic ecosystems. With this information, a conceptual framework can be developed contributing to enhance our attention and concern about human impacts on ecosystems.