The Atchafalaya River Basin is the largest remaining forested wetland in the contiguous United States. Since 1960, dredging and channel erosion in the Basin have resulted in changes to the hydrologic connectivity that have not been quantified. Analyses were conducted to determine the hydraulic and geomorphic factors that have changed since discharge became controlled that may have decreased river/floodplain connectivity. We examined: (1) stage/discharge relationships from 1960 to 2014; (2) hydroperiods across the floodplain; (3) discharge distribution to the floodplain by comparing discharge measurements from 1959–1968 to 2005–2012; and (4) channel cross-sections and floodplain elevations. Our results indicate that much of the floodplain no longer receives headwater discharge (upstream to downstream, > 200 km2) or receives too little discharge to alleviate stagnancy and hypoxia in the forested wetland at lower stages. Large portions of the Basin (400 km2) have low water levels controlled by channel geomorphology and sea-level rise that inundate the forested floodplain for more than 50% of the calendar year. This extended duration of inundation contributes to hypoxia and likely reduces nutrient retention. The confinement of discharge to a large efficient channel compromises the ability of this system to respond to sea-level rise and subsidence. This study provides insight to the effects of flood management projects along Coastal Plain rivers and deltas.