Wetland biogeochemistry varies spatially within distinct hydrologic units. Many coastal wetlands have been diked and managed for habitat provisioning. Management efforts typically aim to control invasive vegetation and encourage native species, yet do not always recognize changes in nutrient cycles due to these actions. We aimed to estimate whole ecosystem sediment-surface water nutrient flux based on weighted measurements in distinct vegetation patches. Our main questions were: 1) Do soils among patches of vegetation differ in sediment-surface water nutrient flux? 2) Is weighting nutrient flux by vegetation patches an effective way to scale this process to the whole ecosystem? And 3) Do complementary methods of measuring sediment-surface water nutrient flux yield similar results? To answer these questions, we collected intact sediment cores (IC) and deployed in situ stacked resin bags (RB) at the same sample points in one hydrologic unit of a coastal wetland adjacent to the western basin of Lake Erie (Magee Marsh, Ohio, USA). We delineated four distinct vegetation patches: grasses, open water, hardwoods, and Typha spp. We then randomly collected three intact sediment cores within each patch and deployed triplicate stacked resin bag cores at the same sample points. The intact sediment cores were incubated for 72 hours, and stacked resin bag cores were retrieved after 14 days. We found that measurements of flux from intact sediment core incubations and stacked resin bag deployments did not always align in regard to direction and magnitude for ammonia (-2.31±8.36 for RB and 18.61±25.07 for IC), nitrate(-0.19±0.69 for RB and -0.86±2.02 for IC), and soluble reactive phosphate (1.06±5.26 for RB and -1.61±4.71 for IC, mean±sd across all sample points, mg/m2/d). Average sediment-surface water nutrient flux was more variable within than among patches for both methods. Underlying wetland processes or characteristics unrelated to dominant vegetation may determine sediment-surface water nutrient flux rates.