The hydrogeochemistry of saline-meteoric water interface zones in sedimentary basins is important in constraining the fluid migration history, chemical evolution of basinal brines, and physical stability of saline formation waters during episodes of freshwater recharge. This is especially germane for interior cratonic basins, such as the Michigan and Illinois basins. Although there are large differences in formation water salinity and hydrostratigraphy in these basins, both are relatively quiescent tectonically and have experienced repeated cycles of glaciation during the Pleistocene. Exploration for unconventional microbial gas deposits, which began in the upper Devonian-age Antrim Shale at the northern margin of the Michigan Basin, has recently extended into the age-equivalent New Albany Shale of the neighboring Illinois Basin, providing access to heretofore unavailable fluid samples. These reveal an extensive regional recharge system that has profoundly changed the salinity structure and induced significant biogeochemical modification of formation water elemental and isotope geochemistry.New-formation water and gas samples were obtained from Devonian-Mississippian strata in the Illinois Basin. These included exploration wells in the New Albany Shale, an organic-rich black shale of upper Devonian age, and formation waters from over- and underlying regional aquifer systems (Siluro-Devonian and Mississippian age). The hydrostratigraphic relations of major aquifers and aquitards along the eastern margin of the Illinois Basin critically influenced fluid migration into the New Albany Shale. The New Albany Shale formation water chemistry indicates significant invasion of meteoric water, with δD values as low as −46.05‰, into the shale. The carbon stable isotope system (δ13C values as high as 29.4‰), coupled with δ18O, δD, and alkalinity of formation waters (alkalinity ≤24.08 meq/kg), identifies the presence of microbial gas associated with meteoric recharge. Regional geochemical patterns identify the underlying Siluro-Devonian carbonate aquifer system as the major conduit for freshwater recharge into the fractured New Albany Shale reservoirs. Recharge from overlying Mississippian carbonates is only significant in the southernmost portion of the basin margin where carbonates directly overlie the New Albany Shale.Recharge of dilute waters (Cl− <1000 mM) into the Siluro-Devonian section has suppressed formation water salinity to depths as great as 1 km across the entire eastern Illinois Basin margin. Taken together with salinity and stable isotope patterns in age-equivalent Michigan Basin formation waters, they suggest a regional impact of recharge of δ18O- and δD-depleted fluids related to Pleistocene glaciation. Devonian black shales at both basin margins have been affected by recharge and produced significant volumes of microbial methane. This recharge is also manifested in different salinity gradients in the two basins because of their large differences in original formation water salinity. Given the relatively quiet tectonic history and subdued current topography in the midcontinent region, it is likely that repeated cycles of glacial meltwater invasion across this region have induced a strong disequilibrium pattern in fluid salinity and produced a unique class of unconventional shale-hosted gas deposits.