This study investigates internal-wave dynamics in the deep Ionian Sea using two unique long-term observational records collected a decade apart (2002–2003 and 2012–2013) at depths exceeding \(2000 \, m\), a region where sustained measurements are extremely limited. These datasets provide a rare opportunity to characterize abyssal variability and to assess how differing background conditions may influence internal-wave properties and mixing. The observations revealed persistent near-inertial and semidiurnal tidal signals at abyssal depths, with a systematic blue-shift of the inertial peak relative to the local Coriolis frequency. The magnitude and spectral structure of this blue-shifted peak differ between the two periods, indicating sensitivity to changes in stratification. In the 2012–2013 record, enhanced spectral energy at the difference frequency \(f - M_{2}\) suggests the presence of nonlinear interactions between inertial and tidal motions. These interactions are accompanied by variations in spectral slopes and episodic increases in inferred vertical diffusivity, often coinciding with intensified near-inertial activity and topographic wave signals likely associated with interactions with steep regional topography. A two-dimensional Korteweg–de Vries internal tide model reproduces key features of the observed variability, supporting the role of bathymetric modulation in shaping the nonlinear internal-wave field and its contribution to the mixing. While the limited hydrographic sampling does not allow a definitive attribution of decadal changes, the contrasting stratification regimes captured by the two records highlight how the complex interaction among the bathymetry, stratification, tide, and internal oscillations significantly modulates internal-wave propagation and mixing within the ocean interior and bottom layer, with implications for understanding long-term energy redistribution and deep-sea variability.