Bayou St. John, an urban water body extending south from Lake Pontchartrain, has two anthropogenic structures that regulate flow from the Lake . The City of New Orleans has plans to remove the inner control structure to improve water quality. Field and numerical methods used in this study show removing this structure increased water elevations throughout the Bayou but resulted in lower water elevation signal amplitudes that caused a lower tidal flow exchange from north to south. Bulk Richardson numbers showed mixing was inversely related to flow and the Bayou generally remains stratified. Resuspension of contaminated sediment could negatively impact the local ecology but predicted shear stress values did not reach a critical value (0.1 N/m2) for resuspension. Removal of the waterfall structure will benefit Bayou St. John by decreasing energy losses from the Lake, however a more pronounced tidal signal from Lake Pontchartrain is required to flush the Bayou.