The Deep-Pelagic Nekton Dynamics of the Gulf of Mexico consortium (DEEPEND) uses observational and multi-model approaches to characterize biophysical variability and investigates the dynamics of deep-pelagic animal assemblages at multiple temporal and spatial scales. Run in near-real time, at 1/25° horizontal-resolution, the HYCOM Gulf of Mexico (HYCOM-GOM) ocean model was used to support the five DEEPEND research cruises (2015-2017) and aid adaptive sampling strategies. Post-cruise, three additional simulations were performed with the HYCOM-GOM configuration to better understand biophysical relationships in the Northeastern Gulf of Mexico. First, a hindcast “nature run” was conducted with no data assimilation. Next two data assimilative runs were completed. One assimilated data from publicly available sources (e.g., the NOAA Global Telecommunication System [GTS]), and the other assimilated in-situ CTD and glider data collected during the cruises. We analyzed the impact of the various assimilated data on the model results and on the characterization of the biophysical habitat and associated environmental drivers.