Water quality impairment and land surface subsidence threaten the viability of the Sacramento-San Joaquin Delta (Delta), a critical component of California’s water conveyance system. Current day irrigation drainage through Delta island peat soils impacts drinking water treatment and is linked to mercury transport, potentially posing both ecological and public health concerns. Hybrid coagulation-treatment wetland systems, termed Chemically Enhanced Treatment Wetlands (CETWs), were studied as a means to cost-effectively treat agricultural drainage water from subsided Delta islands to reduce the export of drinking water quality constituents of concern and mitigate land subsidence through accretion. We provide cost estimates and design recommendations to aid broader implementation of this technology. Over a 20-year horizon using a Total Annualized Cost analysis, we estimate treatment costs of $602 – $747 per acre-foot (ac-ft) water treated and $36 – $70 per kg dissolved organic carbon (DOC) removed depending upon source water DOC concentrations for a small 3-acre CETW system. For larger CETW systems scaled for island sizes of 3,500 – 14,000 acres, costs decrease to $108 – $239 per ac-ft water treated and $11 – $14 per kg DOC removed. The footprints of CETW systems were estimated to be approximately 3% of the area being treated for 4-day hydraulic retention time systems but would decrease to less than 1% for 1-day hydraulic retention time systems. CETWs ultimately address several of the Delta’s key internal issues while keeping water treatment costs competitive with other currently available treatment technologies at similar scales on a per carbon removed basis. CETWs offer a reliable system to reduce out-going DOC and mercury loads and they provide the additional benefit of sediment accretion. System costs and treatment efficacy are highly dependent on inflow source water conditions, land availability and other practical matters. To keep costs low and removal efficacy high, wetland design features will need site-specific evaluation.