Understanding sediment nutrient dynamics in the Milwaukee River Basin is important for assessing water quality and stream habitat. The Milwaukee River is a major tributary to Lake Michigan that provides clean drinking water for over one million people. Urban and agricultural runoff are linked to elevated loads of phosphorus, nitrogen, and sediment in the river. Excessive nutrients can impair water quality and cause excessive phytoplankton and cyanobacteria growth which in-turn can reduce oxygen levels affecting invertebrates and fish, as well as produce toxins harmful to humans and aquatic organisms. In-stream nutrient cycling can lower water column nutrient concentrations and improve water quality; stream sediments can store phosphorus long term and remove nitrogen permanently through microbially-mediated denitrification. However, stream sediments may also release phosphorus to the water column if they are saturated with phosphorus. This study quantified rates of biogeochemical processes in 24 sites within the Milwaukee River Basin and 8 sites outside the Milwaukee River Basin but within the Milwaukee River metropolitan area. Data from this study will provide baseline information about sediment nutrient dynamics in the Milwaukee River Basin and help assess the effectiveness of stream rehabilitation to retain phosphorus and remove nitrogen prior to the water reaching Lake Michigan.