Due to its importance for special status fish, the San Francisco Bay (SFB) estuary has been designated as Essential Fish Habitat (EFH) under the Magnuson-Stevens Fishery Conservation and Management Act ([MSA; 16 U.S.C. 18559b)]. Within this estuary, benthic macroinvertebrate communities provide important prey resources for many economically significant fish species that rely on EFH. Periodic maintenance dredging can impact these infaunal communities; however, there is a lack of scientific information specific to SFB on the degree of benthic community disruption caused by dredging. In addition, rates of benthic community recolonization and recovery following dredging and subsequent effects on foraging fish are unknown. For this reason, it is difficult for regulatory and resource agencies to determine the impacts of maintenance dredging. Thus, the National Marine Fisheries Service (NMFS) and the consortium of agencies (US Environmental Protection Agency (EPA), US Army Corp of Engineers (USACE), San Francisco Regional Water Quality Control Board (SFRWQCB), and San Francisco Bay Conservation and Development Commission (BCDC)) comprising the San Francisco Bay Long Term Management Strategy for Dredging (LTMS) effort identified a study of dredging impacts on SFB fish foraging habitat as one of their highest priorities in their 2011 Programmatic EFH Agreement.