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An agent-based modeling (ABM) framework was developed to support oyster reef restoration efforts in the Caloosahatchee River Estuary located within the encompassing Charlotte Harbor estuarine system, Southwest Florida. The modeling approach is novel for this shallow estuary which experiences heavily managed freshwater inflow known to be an ecological stressor to the estuary's oysters. The aims of the study were to (1) determine the ABM's accuracy in simulating larval dispersal patterns when compared with measured in situ larval settlement data; (2) establish connectivity patterns between various oyster reefs within the estuary; and (3) discover larval transport pathways within the Charlotte Harbor estuarine system. Key characteristics of the ABM, in particular the agents serving as simulated larvae, include settlement behavior and salinity tolerance and associated mortality. The ABM accurately recreated larval dispersal patterns during the peak spawning season, providing fundamental insight into the importance of protecting the furthest upstream oyster reef as a sustained larval source to the downstream reefs. Thus, supporting the effectiveness of using field measurements for the validation of ABMs and subsequently using ABM simulations to bolster future field studies. Ultimately, this study provides an effective, generally applicable, approach to model larval ecology for restoration purposes.