The Bonnet Carré Spillway (BCS) serves as a key flood-control structure on the lower Mississippi River, but its operation introduces substantial freshwater into estuarine systems such as the Mississippi Sound, often disrupting salinity regimes critical to oyster habitat viability. This study integrates physical modeling and a Habitat Suitability Index (HSI) framework to evaluate how variations in riverine inflow magnitude and spillway operation scenarios impact oyster habitat suitability across biological life stages and seasonal cycles. 
Using the msbCOAWST modeling system, we simulated observed and alternative BCS scenarios from 2018 to 2020, focusing on the double openings of 2019. Scenario variations included discharge thresholds (e.g., 1.2–1.25 million cfs at Baton Rouge), shortened or without second opening, and modified pacing of spillway operations. Twin simulations using distinct river datasets enabled sensitivity analysis under contrasting freshwater inputs. 
HSI scores were calculated for four oyster life stages (larval, spat, seed, sack) using daily surface and bottom salinity at ecologically significant reefs across the Western, Central, and Eastern Mississippi Sound. Results showed that Case 2, which reduced freshwater diversion from 572% to 86% of Lake Pontchartrain’s volume, significantly improved salinity conditions and habitat suitability—especially during the critical summer and fall periods. Seasonal-averaged HSI scores revealed that Western and Central Sound reefs experienced the greatest benefit under modified scenarios, indicating the potential for improved ecological outcomes through adaptive flow management. 
This work highlights the significance of integrated modeling to inform operational strategies that balance flood control with estuarine ecosystem resilience, providing a transferable tool to support coastal resource management under future climate and hydrological uncertainty.