Expansion of agriculture in the Brazilian Amazon has been driven not just by demands from traditional, rural producers, but also large agriculture and cattle producers, both of whom have put considerable pressure on remaining forests and their watersheds. Monitoring of these watersheds has been a focus of intensive study for the past 20 years and although this work has greatly increased our understanding, considerable gaps still remain in our ability to provide adequate recommendations for land management and associated public policies. In this study we present a summary of findings from these previous results. For small properties, the use of fire to prepare land for cultivation remains controversial, while in large properties, forest conversion to pasture and/or crop production has had a meaningful and adverse effect on water quality. Riparian forest conservation can make a significant difference in reducing impacts of land-use change. Secondary vegetation can also play an important role in mitigating these impacts. New types of sustainable agricultural production systems, together with incentives such as payments for ecosystem service can also contribute. Continued monitoring of these changes, together with robust sustainable development plans, can help to preserve forest while still addressing the social and economic needs of Amazonian riverine inhabitants.