The evolution of sedimentary basins separated by uplifted topographic barriers is characterised by gradual regressive deposition until one of the basins is filled and its sedimentation bypasses to the adjacent basin, defining a depositional shift. One of the critical parameters controlling these depositional shifts is sea level variation, its drop potentially triggering a depositional shift by cancelling the available accommodation space. Conversely, a sea level rise can create new accommodation space resulting in a depositional shift towards a previously overfilled basin. Here we use a three dimensional numerical model to study the sedimentary response to sea level variations of a system of two basins. In this model, a single mountainous source area is feeding an intra-continental basin that is separated by a submarine barrier from another basin with normal marine bathymetry. The sedimentary response is modelled during a cycle of sea-level drop and subsequent rebound that exposes the barrier to sub-aerial erosion. The examined parameters are the barrier height, magnitude and duration of sea level change, climate and flexural rigidity. Modelling demonstrates that shifting the bulk of sedimentation from the continental basin to the open marine environment requires some minimum magnitudes and durations of sea level drop. Moreover, given the specific geometry and parameters of our model, an intervening barrier causes a delay of up to 0.35 Myr, depending on the magnitude and duration of sea level change, to the onset of an outward depositional shift when compared to a situation without a barrier. These depositional shifts depend on changes in climate, magnitude and duration of sea level change. Model results are applied to the connectivity between the Black Sea and the Dacic Basin, suggesting that depositional shifts observed during the Messinian Salinity Crisis can be explained by a sea level drop of > 1000 m in the Black Sea.