Watershed land cover affects in-stream water quality and sediment nutrient dynamics. The presence of natural land cover in the riparian zone can reduce the negative effects of agricultural land use on water quality; however, literature evaluating the effects of natural riparian land cover on stream sediment nutrient dynamics is scarce. The objective of this study was to assess if stream sediment phosphorus retention and nitrogen removal varies with riparian forest cover in agricultural watersheds. Stream sediment nutrient dynamics from 28 sites with mixed land cover were sampled three times during the growing season. Phosphorus dynamics and nitrification rates did not change considerably throughout the study period. Sediment total phosphorus concentrations and nitrification rates decreased as riparian forest cover increased likely due to a decline in fine, organic material. Denitrification rates were strongly correlated to surface water nitrate concentrations. Denitrification rate and denitrification enzyme activity decreased with an increase in forest cover during the first sampling period only. The first sampling period coincided with the greatest connectivity between the watershed and in-stream processing, indicating that riparian forest cover indirectly decreased denitrification rates by reducing the concentrations of dissolved nutrients entering the stream. This reduction in load may allow the sediment to maintain greater nitrogen removal efficiency, because bacteria are not saturated with nitrogen. Riparian forest cover also appeared to lessen the effect of agriculture in the watershed by decreasing the amount of fine material in the stream, resulting in reduced phosphorus storage in the stream sediment.