Agricultural activities are essential for the supply of food and biofuel; however, it is one of the main land uses that cause water quality degradation. Thus, forest conservation strategies are essential to ensure water quality in agricultural watersheds. However, land-use pattern at multiple scales has an impact on the relationship between forest, agriculture, and water quality. To understand these multiscale impacts of forest conservation on water quality, we conducted several studies in Brazilian agricultural watersheds in the Atlantic Forest comparing land-use/land-cover pattern at different scales on various water quality variables, including nutrients, sediments, and microorganisms. Riparian vegetation has a great influence on the removal of nitrogen, phosphorus, reduction of pesticides and sediments loading, as well as providing shade and food for the aquatic ecosystem. The conversion of riparian forests to agricultural lands has resulted in reduced water quality and functional processes. The main impacts included water temperature increase, riverbanks erosion causing sediment input, and the increase of nutrients, pesticides, and sediments load to streams. Water quality parameters associated with runoff (eg phosphorus, nitrogen, organic carbon, fine sediments and other pollutants) from agricultural lands have been linked to land-use/land-cover pattern at catchment scale. Our studies also showed that for watersheds with the same land-use composition and percentage of native vegetation, greater vegetation fragmentation negatively altered water quality in agricultural catchments. We found high concentrations of nitrate in streams with riparian forest, possibly caused by the level of riparian forest fragmentation. Streams in watersheds dominated by sugarcane had nitrate, conductivity and dissolved carbon altered because of deforested headwaters. Therefore, in addition to the protection of riparian zones, it is necessary that the watershed management in Brazil considers the protection of other areas of native vegetation that are important for the maintenance of the hydrological, biogeochemical and biological cycles.