Upper Mississippi River Basin Protection Act

Upper Mississippi River Basin Protection Act - Requires federal investments in the Upper Mississippi River Basin to be guided by accepted and documented scientific methods and to take into account the results of studies using such methods to identify and quantify the sources, transport, and fate of nutrients and sediment and to quantify the effect of treatment methods or conservation measures on nutrient and sediment management.

Directs the Secretary of the Interior, as part of an Upper Mississippi River Stewardship Initiative and acting through the U.S. Geological Survey (USGS), to establish a nutrient and sediment monitoring network for the Basin.

Directs the Secretary to: (1) establish guidelines for related data collection and storage activities; (2) inventory the sediment and monitoring efforts of governmental, tribal, and nongovernmental entities for the purpose of creating a baseline understanding of overlap, data gaps, and redundancies; (3) integrate such monitoring efforts into the sediment and nutrient monitoring network; and (4) collaborate with other public, tribal, and private monitoring and assessment programs in establishing the monitoring network.

Directs the National Research Council of the National Academy of Sciences to conduct a water resources assessment of the Basin.

Requires the Director of the USGS: (1) as part of the Initiative, to develop and implement a plan to improve existing water-quality models to identify and quantify significant sources of sediment and nutrients in the Basin at the subwatershed scale; (2) to establish a communication plan that includes use of the Internet to provide information on accomplishments of public and private programs designed to manage sediment and nutrients in the Basin and on seasonal and annual concentrations and loads of sediment and nutrients in the Upper Mississippi River and its tributaries; and (3) provide an annual report that includes information on concentrations and loads of nutrients and sediment derived from monitoring activities conducted in the Basin.