The Fox River transports elevated loads of nitrogen and phosphorus to Lake Michigan. The increased concentration of N and P causes eutrophication of the lake, creating hypoxic zones and damaging the lake ecosystem.To decrease loading, best management practices (BMPs) have been implemented in the uplands of the basin. Little work has been done, however, to reduce nutrient concentrations in the river. Rivers are capable of removing nutrients through biotic uptake and sediment burial and are able to remove N through denitrification. Identifying and managing these locations of increased nutrient cycling known as “hot spots” may be another mechanism for nutrient mitigation.Our objective was to identify hot spots of N and P cycling in the Fox River basin. We measured rates of specific biogeochemical processes (e.g. ambient and potential denitrification, and sediment phosphorus uptake and release) at sites that had varying mixed land use. We also measured variables that are known to affect nitrogen and phosphorus cycling. Models were created to estimate how land use type and BMP coverage can effect the capacity of the Fox River and its tributaries to retain and cycle N and P.