The effects of sediment, ground-water, and surface-water processes on the timing, quantity, and mechanisms of N and P fluxes were investigated in the Wood River Wetland 5–7 years after agricultural practices ceased and seasonal and permanent wetland hydrologies were restored. Nutrient concentrations in standing water largely reflected ground water in winter, the largest annual water source in the closed-basin wetland. High concentrations of total P (22 mg L⁻¹) and total N (30 mg L⁻¹) accumulated in summer when water temperature, air temperature, and evapotranspiration were highest. High positive benthic fluxes of soluble reactive P and ammonium (NH₄ -N) were measured in two sections of the study area in June and August, averaging 46 and 24 mg m⁻² d⁻¹, respectively. Nonetheless, a wetland mass balance simultaneously indicated a net loss of P and N by assimilation, denitrification (1.1–10.1 mg N m⁻² h⁻¹), or solute repartitioning. High nutrient concentrations pose a risk for water quality management. Shifts in the timing and magnitude of water inflows and outflows may improve biogeochemical function and water quality by optimizing seed germination and aquatic plant distribution, which would be especially important if the Wood River Wetland was reconnected with hyper-eutrophic Agency Lake.