Water mass generation and mixing in the eastern Fram Strait are strongly influenced by the interaction between Atlantic and Arctic waters and by the local atmospheric forcing, which produce dense water that substantially contributes to maintaining the global thermohaline circulation. The West Spitsbergen margin is an ideal area to study such processes. Hence, in order to investigate the deep flow variability on short-term, seasonal, and multiannual timescales, two moorings were deployed at ~1040 m depth on the southwest Spitsbergen continental slope. We present and discuss time series data collected between June 2014 and June 2016. They reveal thermohaline and current fluctuations that were largest from October to April, when the deep layer, typically occupied by Norwegian Sea Deep Water, was perturbed by sporadic intrusions of warmer, saltier, and less dense water. Surprisingly, the observed anomalies occurred quasi-simultaneously at both sites, despite their distance (~170 km). We argue that these anomalies may arise mainly by the effect of topographically trapped waves excited and modulated by atmospheric forcing. Propagation of internal waves causes a change in the vertical distribution of the Atlantic water, which can reach deep layers. During such events, strong currents typically precede thermohaline variations without significant changes in turbidity. However, turbidity increases during April–June in concomitance with enhanced downslope currents. Since prolonged injections of warm water within the deep layer could lead to a progressive reduction of the density of the abyssal water moving toward the Arctic Ocean, understanding the interplay between shelf, slope, and deep waters along the west Spitsbergen margin could be crucial for making projections on future changes in the global thermohaline circulation.