We used conservative isotope tracers (deuterium and oxygen-18) and biologically relevant water quality measurements to assess connectivity of the Atchafalaya River to other waterways in its floodplain during the rising limb, peak, and falling limb of the 2011 flood pulse. We compared isotope tracers and water quality (dissolved oxygen and specific conductance) in biweekly samples at 83 sites in two areas that differed in their connectivity. We also compared tracers to an 8-year dataset of water quality measurements from the same sites. Although tracers clearly described differences in connectivity between the two floodplain areas and were correlated with concurrent measures of water quality, relationships were mediated by a strong temporal component and site-level variation in aquatic vegetation. Our results suggest a delay in floodplain water quality response to water inputs, and a strong influence of aquatic vegetation that locally overwhelms connectivity as a primary driver of local water quality.