We used available data to estimate changes in land use and wet, non-farmable, and marginally farmable (WNMF) areas in the Delta from 1984 to 2012, and developed a conceptual model for processes that affect the changes observed. We analyzed aerial photography, groundwater levels, land–surface elevation data, well and boring logs, and surface water elevations. We used estimates for sea level rise and future subsidence to assess future vulnerability for the development of WNMF areas. The cumulative WNMF area increased linearly about 10-fold, from about 274 hectares (ha) in 1984 to about 2,800 ha in 2012. Moreover, several islands have experienced land use changes associated with reduced ability to drain the land. These have occurred primarily in the western and central Delta where organic soils have thinned; there are thin underlying mud deposits, and drainage ditches have not been maintained. Subsidence is the key process that will contribute to future increased likelihood of WNMF areas by reducing the thickness of organic soils and increasing hydraulic gradients onto the islands. To a lesser extent, sea level rise will also contribute to increased seepage onto islands by increasing groundwater levels in the aquifer under the organic soil and tidal mud, and increasing the hydraulic gradient onto islands from adjacent channels. WNMF develop from increased seepage under levees, which is caused by changing flow paths as organic soil thickness has decreased. This process is exacerbated by thin tidal mud deposits. Based primarily on projected reduced organic soil thickness and land–surface elevations, we delineated an additional area of about 3,450 ha that will be vulnerable to reduced arability and increased wetness by 2050.