Fluvial-tidal wetlands in the Ni-les’tun Unit (~200 hectares) of the Bandon Marsh, Coquille Estuary, Oregon, were analyzed for shallow aquifer conditions that could influence surface water-qualities in reconstructed marsh, pond, and discharge/tidal channels. The wetlands were surveyed for pre-historic channel features, depth to groundwater surface (GWS), and subsurface salinity intrusion by ground penetrating radar (GPR) in 50 profiles, totaling 11.1 km in track line distance. Only small flood-discharge/tidal channel features (<10 m width and 1–2 m depth) were recorded in the interior floodplain areas. GWS reflections were observed at 0.5–2.0 depth, where the GPR signal was not obscured by localized salinity intrusion (~0.5 km landward distance) from the adjacent Coquille Estuary channel. Top-sealed piezometers (1.5–2.0 m depth) were installed at 10 sites, where in-situ groundwaters were monitored for temperature (8.5–16.5° C), conductivity (<100–18,800 μS cm-1), and pH (2.5–7.8) on a seasonal basis. Dissolved oxygen was semi-quantitatively measured (ChemSticks) at some sites, and all sites were monitored (fall, winter, summer) for GWS level. Low dissolved oxygen (DO <1 ppm) at four sites was of particular concern for potential discharge into small channels that were to be constructed for juvenile salmonid nursery habitat. The horizontal and vertical asymmetries of conductivity (salinity), used as a conservative groundwater source tracer, and measured GWS elevation trends (gradients) led to a four-part flow model for shallow groundwater supply in the Ni-les’tun floodplain. Freshwater supplied, in part, by hillslope discharge contributes to low pH and low DO water quality in the shallow aquifer. Saline water, supplied by subsurface salinity intrusion and evaporative capillary rise, could introduce salinity toxicity to isolated (stagnant) surface ponds. Following construction of a dense channel network (2009–2011) by the Bandon Marsh National Wildlife Refuge, selected Ni-les’tun channel waters (13 sites) were monitored (2011-2012) for resulting water-quality. The tidally-connected channels generally showed improved water-quality relative to groundwater in some nearby piezometer sites. However, low-quality groundwater supply compromised some channel reaches (DO ~2.0–4.7 ppm) that depended on groundwater recharge from hillslope discharge during either summer or winter conditions.