The density field in Narragansett Bay (NB), a northeast U.S. estuary with complex geometry that suffers hypoxia, is described and related to driving factors using monthly means from time series observations at 9 sites during late spring to early fall 2001–2009. Stratification (deep-shallow density difference) is dominated by salinity and strongest (4–7 kg m−3 in late spring) near rivers in the north and east. Shallow horizontal density gradients are about 0.2 kg m−3 km−1; deep densities have minor spatial and seasonal variations. Geographic structure in density, and its inter-annual anomalies, is weaker than expected based on the complex geometry and large size relative to the internal deformation radius. Inter-annual variability is primarily driven by river flow and weakly influenced by winds, contrasting nearby systems (Chesapeake Bay, Long Island Sound), likely due to reduced fetch and/or unfavorable alignment with prevailing winds. Stratification response to river flow follows 2/3 power scaling despite that the theory omits important NB attributes (complex geometry, depth-varying horizontal gradients). Contrasting other systems (Delaware Bay, San Francisco Bay), horizontal gradients are at least as responsive to river forcing as theoretical 1/3 power scaling; depth-dependent horizontal gradients or finite basin constraint of intrusion length may be responsible. Bay-wide inter-annual variations in seasonal hypoxia correlate with late spring stratification, though stratification peaks in the north and east with hypoxia most severe in the north and west. Long-term response of stratification, and thus its role in hypoxia, to climate-driven increases in river flow and temperatures will be dominated by the former.