Extensive canyons, excavated into the margins of the Levant Basin during the Oligocene–Miocene, are interesting case-studies for canyon fills in carbonate settings. The carbonate Pattish Formation, developed along the margins of the pre-evaporitic Messinian Beer Sheva Canyon in Israel, was investigated using both onshore seismic imaging and field data. The canyon has three main seismic facies of fill (1) Subparallel reflections mimicking the canyon´s morphology; (2) chaotic reflections overlying the subparallel ones, and (3) sigmoidal reflections, locally with sharp edges at the canyon margins. The first seismic facies corresponds to the pelagic marls of the Bet Eshel Formation. The other two seismic facies are, respectively, equivalent to bioclastic calcarenite clinobeds with slumps and channels, and to coral–stromatolite reefs and reef slopes of the Pattish Formation observed at outcrop. There were three phases of canyon development: (1) slope incision and headward erosion due to tectonic uplift and eustatic sea-level fall during the Early Oligocene, and large slope failure during the latest Middle Miocene; (2) platform incision and connection with a fluvial system in the Late Miocene related to falling sea level and tectonic uplift; and (3) canyon filling first by pelagic marls at the centre of the canyon, followed by calcarenite clinobeds at the canyon flanks formed by gravity flows. Finally, carbonate production at the margins of the canyon resulted in reefs and associated slopes prograding towards the canyon axis. The late canyon filling phase ended with the deposition of evaporites during the Messinian Salinity Crisis.