Deep (> 1000 m depth) barotropic mesoscale eddies contribute to Loop Current Eddy (LCE) separation events, but sparse deep observations in the Gulf of Mexico limit our dynamical understanding and forecast skill. Data from a regional HYbrid Coordinate Ocean Model (HYCOM) free-running simulation are used to analyze deep, mesoscale variability over an 18-year period in the Eastern Gulf. A spectral analysis reveals three notable frequency bands: 1/150–1/30 days^-1, 1/60–1/30 days^-1, and 1/30–1/10 days^-1. 60–150 day variance is concentrated in the central Eastern Gulf and the Deep Southeast Channel (DSC), whereas 30–60 day variance is strongest near the Mississippi Fan. Complex empirical orthogonal function analysis identifies three modes that contain 65 % of the total deep variance. The first mode is associated with 30–60 day eddies formed by baroclinic development near the Mississippi Fan and propagate into the Eastern Gulf basin, then westward; the second and third modes capture variance representative of eddies in the 60–150 day and 10–30 day bands. Periods of largest modal amplitudes coincide with times when the LC extends into the Gulf, indicating that the deep Eastern Gulf is energized by the LC via baroclinic development and topographic interactions. The presence of a strong deep cyclone in the DSC is associated with Modes 2 and 3; LCE separations coinciding with this feature occur south of 25° N. Insights from this work suggest greater emphasis in observing the DSC to improve the predictability of LCE separations, and our understanding of the physical mechanisms controlling these events.