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Accurate high-resolution ocean models are required for hurricane and oil spill pathway predictions, and to enhance the dynamical understanding of circulation dynamics. Output from the 1/25° data-assimilating Gulf of Mexico HYbrid Coordinate Ocean Model (HYCOM31.0) is compared to daily full water column observations from a moored array, with a focus on Loop Current path variability and upper-deep layer coupling during eddy separation. Array-mean correlation was 0.93 for sea surface height, and 0.93, 0.63, and 0.75 in the thermocline for temperature, zonal, and meridional velocity, respectively. Peaks in modeled eddy kinetic energy were consistent with observations during Loop Current eddy separation, but with modeled deep eddy kinetic energy at half the observed amplitude. Modeled and observed LC meander phase speeds agreed within 8% and 2% of each other within the 100-40 and 40-20 day bands, respectively. The model reproduced observed patterns indicative of baroclinic instability, that is, a vertical offset with deep stream function leading upper stream function in the along-stream direction. While modeled deep eddies differed slightly spatially and temporally, the joint development of an upper-ocean meander along the eastern side of the LC and the successive propagation of upper-deep cyclone/anticylone pairs that preceded separation were contained within the model solution. Overall, model-observation comparison indicated that HYCOM31.0 could provide insight into processes within the 100-20 day band, offering a larger spatial and temporal window than observational arrays.