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Stormwater management retrofit projects such as bioretention systems, constructed wetlands, and extended detention basins have long been recognized as tools for removing pollutants from urban stormwater runoff. However, stormwater retrofits, if designed correctly, can also achieve substantial reductions channel-derived sediment and phosphorus loading (e.g., bank erosion) by moderating in-channel shear stresses during erosion producing events. Through a series of case studies, the author details the methodological challenges associated with optimizing stormwater retrofit design to achieve reductions in channel-derived sediment and phosphorus loading. Several specific aspects of these challenges will be presented. First, the difficulties in obtaining accurate and reliable estimates of critical shear stress within natural stream channels will be reviewed. This discussion will include a review of the various in situ methods used to measure critical shear stress for cohesive bank material and incipient motion formulae used to estimate critical shear stress for non-cohesive bed material. Second, the author will discuss the challenges associated with relating hydraulic metrics (e.g. excess shear stress, etc.) with rates of stream bank erosion in natural stream systems. Third, the author will review hydrologic/hydraulic modeling options for quantifying the effects of stormwater retrofits on in-channel hydraulic conditions and, ultimately, on bank and bed erosion rates. The author will also comment on the broader policy challenges associated with crediting in-channel sediment and phosphorus load reductions achieved through stormwater retrofit projects. Finally, the author will discuss research and development initiatives required to improve the ability of practitioners to reliably estimate channel-derived pollutant load reductions associated with stormwater retrofit projects.