The Blue Earth River (BER) basin is a major contributor of sediment and nutrients to the Minnesota River. The BER and its' tributaries (including Elm Creek) are impaired for turbidity. This research investigated the sources, movement and storage of sediment and nutrients from subwatersheds and channels of Elm Creek. Inflow from corn-soybean fields was compared with outflow from restored wetland-perennial vegetation complexes; flashy surface runoff into a wetland complex carried high concentrations of sediment and Phosphorous (P). Subsurface tile flow from croplands carried 75-90% of flow volume into the wetland, with NO₃-N concentrations of 17-19 mg/1. The wetland complexes reduced peak flows and annual total suspended solids (TSS) by over 90% and reduced NO₃-N outflow to zero during the growing season, but were less effective at removing P due to residual nutrients in pond sediments. In-stream sampling showed that suspended volatile solids (SVS) contributes to turbidity in channel reaches receiving inflow from eutrophic lakes. SVS comprises 14-100% of TSS in channels and lake outlets, with higher percentages during late summer baseflow. Turbidity and suspended sediment increased with flow in high runoff periods and was affected by channel morphologic features. Turbidity increased non-linearly downstream sharply rising past Creek Lake. Increasing stream power and entrenchment with excess sediment supply promote high turbidity levels in lower Elm Creek. Widespread channel instability was characterized by frequent mass-wasting, channel entrenchment and lateral migration rates of up to 1.8 m/year. Increased streamflow from drainage, loss of sinuosity from channelization, straightening at road crossings and natural cutoffs all contributed to channel entrenchment. Modeling showed that entrenchment reduces the frequency of over-bank sediment deposition while increasing sediment transport, aggravating turbidity problems. Fine-grained sediment was stored in headwater ditches, lakes and wetlands (median depth 0.3-1 m), with significantly less sediment accumulation in lower reaches, in opposition to the standard pattern of deposition near the river mouth. Land-use, drainage alteration and channel adjustment are integrally linked and will need to be addressed to meet turbidity and related TMDLS. Towards that goal, an integrated riparian agroecosystem for reducing channel erosion while maintaining agricultural uses is presented.