Drowned river mouth lakes are major features of coastal Great Lakes habitats and may influence nutrient and organic matter contributions from watersheds to near shore coastal zones. In May through October 2003, we measured loads of nutrients, surficial sediment, and seston to track the delivery of riverine-derived materials from the lower Muskegon River Watershed (MRW) into the near shore area of southeast Lake Michigan. Nutrient flux data indicated that seasonal loads of 1800metrictons (MT) of particulate organic carbon, 3400MT of dissolved organic carbon, and 24MT of total phosphorus were discharged from the lower Muskegon River, with approximately 33% of TP load and 53% of the POC load intercepted within the drowned river mouth terminus, Muskegon Lake. Carbon: phosphorus molar ratios of seston in Muskegon River (C:P=187) and Muskegon Lake (C:P=176) were lower than in Lake Michigan (C:P=334), indicating phosphorus limitation of phytoplankton in near shore Lake Michigan. Isotopic signatures of seston collected in Muskegon Lake were depleted in δ13C (−30.8±1.6‰) relative to the isotope signatures of seston from Lake Michigan (−26.2±1.3‰) or the mouth of the Muskegon River (−28.1±0.5‰), likely due to the presence of biogenic methane in Muskegon Lake. Seston δ15N increased on a strong east-to-west gradient within Muskegon Lake, indicating significant microbial processing of nutrients. The extent of nutrient uptake in Muskegon Lake altered the chemical and isotopic characterization of seston flowing into Lake Michigan from Muskegon River.