Contemporary land use can affect sediment nutrient processes in rivers draining heavily modified watersheds; however, studies linking land use to sediment nutrient processes in large river networks are limited. In this study, we developed and evaluated structural equation models (SE models) for denitrification and phosphorus retention capacity to determine direct and indirect linkages between current land use and sediment nutrient processes during baseflow in the Fox River watershed, Wisconsin USA. A large spatial-scale dataset used for this study included sediment nitrogen and phosphorus retention measurements and land use information for 106 sites. The SE models for the Fox River watershed identified direct links between current land use and in-stream sediment nutrient processes. Sub-watersheds with agricultural land consisting of more natural land cover had lower surface water nitrate concentrations and higher denitrification enzyme activity than sub-watersheds with less alternative cover. This suggests that best management practices implemented in the Fox River watershed that restore natural land cover can improve water quality through nitrogen removal on the agricultural landscape and in the river network. Best management practices are not having the same measurable affect on phosphorus in the river network, most likely due to legacy phosphorus stored in the sediment.