Wetlands are widely recognized as nutrient sinks for their ability to remove nutrients in runoff and retain them in soils. This is a valuable service, especially in agricultural watersheds, making nutrient removal one of the main goals in many wetland creation and restoration projects. However, incorporating nutrient management considerations requires site-level assessments, the scale at which wetland creation and restoration occur. Here we studied how carbon (C) sequestration, and nitrogen (N) and phosphorus (P) accumulation vary at different microtopographic levels and locations within a freshwater, estuarine marsh on the coast of Lake Erie. We further explored links between C sequestration, and N and P accumulation in recent years, and orthophosphate (PO43−), ammonium (NH4+), and nitrate (NO3−) concentrations and loads. The rates of C sequestration and N accumulation were relatively lower at spots of intermediate depth and locations closer to the wetland’s main channel. P accumulation was highest at deep spots but did not differ among locations based on distance from the channel. Empirical models showed that nitrate load is the most important variable explaining the variability in C, N, and P sequestration/accumulation (r2 = 0.57, 0.61, and 0.32, respectively) and that the relationship between inorganic nutrient loads and accumulation was negative. Our findings suggest that including microtopographic relief features in wetland creation and design, especially deeper spots, is critical to enhancing wetland ecosystems’ C, N, and P sinking capacity. Also, that upstream nitrate management should be a priority to increase benefits from C sequestration and long-term N and P accumulation.