The study of the relationship between the upper and lower layers in the Gulf of Mexico (GoM) has experienced a lot of progress in recent years. Nevertheless, an examination of this coupling for the entire GoM in a statistically consistent manner is still needed. Layer thickness data from a GoM 21-year free-running simulation is used to examine the coupling between the upper (<250 m) and lower (>1000 m) layers with focus on the dominant modes of variability through a Hilbert Empirical Orthogonal Functions (HEOFs) analysis. The three leading modes of the upper layer are associated with the Loop Current’s (LC) lifecycle and LC eddy (LCE) shedding, with lower-layer variability vertically corresponding and intensified along certain bathymetric features. These modes are periodic, indicating recurrence of circulation patterns in agreement with observations. The fourth mode of the upper layer is associated with the translation of LCEs and their dissipation in the northwestern GoM, which significantly contributes to a richer lower-layer variability in a vast area of the western GoM. The lower mode describes the deep anticyclone-cyclone accompanying the LCEs, the strengthening of the circulation along the Sigsbee Gyre western branch, and the variability over the Sigsbee plain. It does not show cyclicity, suggesting persistence of the associated circulation patterns with a dominant timescale of 14 months. Evidence and corroboration of recently observed lower-layer circulation features are provided. The application of the HEOFs technique used here can complement the three-dimensional oceanic assimilation methods by projecting surface information to depth in a physically consistent manner.