Lake water level fluctuations are an important factor driving variation in many ecosystem processes. The nearshore sediments that are periodically exposed and re-inundated can develop distinct physical and chemical characteristics, especially in relationship to the organic matter content of the sediments and the particle size distribution. These sediment characteristics in turn can alter the flux of nitrogen (N) and phosphorus (P) from sediments into the water column when sediments are inundated. Here, we used intact sediment core experiments across a range of sediment inundation frequencies to estimate the effect of inundation frequency on sediment nutrient flux in Kabetogama Lake, Minnesota, USA. We observed associations between elevation or inundation frequency and some sediment characteristics, but in a structural equation model, inundation frequency and the sediment properties we measured were poorly related to inorganic nutrient flux. On the other hand, inundation frequency did have a moderate association with organic N and P flux from sediments, which could be due to decay of terrestrial organic matter that accumulates on exposed sediments. We used our parameterized structural equation model to estimate how three different water level management regimes employed over the past 50 years could influence organic N and P flux from sediments. The models suggested more recent water level management regimes reduced organic N and P flux by 9%–13% and 5.9%–9.8%, respectively. Nearshore sediment flux could sustain and influence harmful algal blooms that occur in this lake, and these fluxes could be influenced by water level management.