The Sacramento-San Joaquin Delta's (Delta) beneficial uses for humans and wildlife are impaired by elevated methylmercury (MeHg) concentrations in fish. MeHg is a neurotoxin that bioaccumulates in aquatic food webs. The total maximum daily load (TMDL) implementation plan aimed at reducing MeHg in Delta fish obligates dischargers to conduct MeHg control studies. Over 150 stakeholders collaborated to identify 24 management practices (MPs) addressing MeHg nonpoint sources (NPS) in three categories: biogeochemistry (6), hydrology (14), and soil/vegetation (4). Land uses were divided into six categories: permanently and seasonally flooded wetlands, flooded and irrigated agricultural lands, floodplains, and brackish-fresh tidal marshes. Stakeholders scored MPs based on seven criteria: scientific certainty, costs, MeHg reduction potential, spatial applicability, technical capacity to implement, negative impacts to beneficial uses, and conflicting requirements. Semi-quantitative scoring for MPs applicable to each land use (totaling >400 individual scores) led to consensus-based prioritization. This process relied on practical experience from diverse and accomplished NPS stakeholders and synthesis of 17 previous studies. Results provide a comprehensive, stakeholder-driven prioritization of MPs for wetland and irrigated agricultural land managers. Final prioritization highlights the most promising MPs for practical application and control study, and a secondary set of MPs warranting further evaluation. MPs that address hydrology and soil/vegetation were prioritized because experiences were positive and implementation appeared more feasible. MeHg control studies will need to address the TMDL conundrum that MPs effective at reducing MeHg exports could both exacerbate MeHg exposure and contend with other management objectives on site.