Low-order streams are important places for river formation and are highly vulnerable to changes in terrestrial ecosystems. Thus, the land-use/land-cover plays an important role in the maintenance of water quality. However, only land-use/land-cover composition may not explain the spatial variation in water quality, because it does not consider land-use/land-cover configuration and forest cover pattern. In this context, the study aimed to evaluate the forest cover pattern effects on water quality on low-order streams located in an agricultural landscape. Applying a paired watershed method, we selected two watersheds classified according to their morphometry and average slope to discard other physical factors that could influence the water quality. Land-use/land-cover pattern was analyzed for composition and forest cover configuration using landscape metrics, including the riparian zone composition. Water quality variables were obtained every two weeks during the hydrological year. This way, watersheds had similar morphometry, slope, and land-use/land-cover composition but differed in forest cover pattern. Watershed with more aggregated forest cover had a better water quality than the other one. The results show that forest cover contributes to water quality maintenance, while forest fragmentation influences the water quality negatively, especially in sediment retention. Agricultural practices are sources of sediment and nutrients to the river, especially in steep relief. Thus, in addition to land-use/land-cover composition, forest cover pattern must be considered in management of low-order streams in tropical agricultural watersheds.