Agroforestry is crucial for improving water quality deteriorated by anthropogenic activities due to the use of chemical substances, including nitrogen (N) and phosphorous (P) in modern agricultural practices (MAPs). This state-of-the-art review aims to revise the influence of agroforestry systems (AFS) on climate change, soil conservation, and groundwater quality. The novelty of this review is that AFS can improve water quality, reduce nutrient loss, and support the biological, chemical, and physical properties of the soil. It is worth noting that the surficial geologic controls, slope gradient, soil types, and topographical conditions are factors that alter a watershed dominated by agroforestry areas. In addition, anthropic aspects, including agricultural practices, can also cause loss of water quality in basins dominated by an AFS area. The novelty of this review also outlines that AFS can be used for the phytoremediation of contaminated soils to reduce aluminum (Al), mercury (Hg), and cadmium (Cd), among others. Therefore, AFS can be used for water decontamination, climate change mitigation, climate adaptation, and soil conservation. More research is needed to investigate the contribution of AFS for soil integrity.