In the Late Miocene–Early Pliocene Lake Pannon, regression went on for about 6Ma. Sediments arriving from the Alpine–Carpathian source area were partly accumulated on the flat-lying morphological shelf of the lake, whereas other portions of the sediment were passing through to the slope and deposited on the deep basin floor. The height of the slope exceeded 400–500m based on correlated well and seismic data. An extended 3D seismic volume covering the Makó Trough, one of the largest and deepest depressions within the Pannonian Basin, provided an opportunity to study sequences and shelf-margin trajectories generated as a result of continuous slope advancement. The lithology of these shelf, slope and basin centre deposits was inferred from seven well logs and 220m core material.In the Makó Trough the southeastward migrating shelf-margin was formed by alternating aggradational and progradational clinothems. Aggradational clinothems, i.e. aggradation accompanied by subordinate progradation, are characterised by rising shelf-margin trajectories. The shelf built up from inner-shelf to shelf-edge deltaic lobes which compose a few dozen metre thick coarsening-up units. The majority of the sand, however, was transported by effective turbidity currents through leveed channels into the basin, and deposited as thick, extended slope-detached turbidite lobes up to a distance of 30km from the shelf edge. In aggradational clinothems both the shelf and the basin floor accreted vertically. Development of progradational clinothems resulted in horizontal (flat) shelf-margin trajectories. Corresponding reflections toplap at the shelf edge and downlap within a distance of few kilometres from the toe of the slope. The shelf was bypassed, sediments accumulated on the slope and directly at the slope–toe region as small simple lobes. Short-distance transport was the result of clay-poor, non-effective turbidity currents. Consequently, the thickness of coeval basin-centre sediments remained negligible in progradational clinothems.Alternations of rising and horizontal shelf margin trajectories indicate that the climate- and subsidence-controlled lacustrine base-level rose continuously, though at varying rates. Descending trajectories were not observed. It means that base-level drops larger in amplitude than the seismic resolution (20–30m), did not occur during the studied time interval, i.e. at 7–5Ma ago, approximately corresponding to the Messinian age. As a result, major forced-regressive wedges or lowstand fans did not develop. This is in contrast with former stratigraphic models claiming that several 3rd-order sequences, including the intra-Messinian unconformity supposedly induced by hundred metres large lake-level drop, developed in Lake Pannon with significant volume of lowstand deposits as turbidites. Instead, aggradational and progradational clinothems are interpreted as fourth-order transgressive, early and late highstand systems tracts. These incomplete sequences represent less than 100kyr time intervals.Due to climate control both on high rate of sediment supply and the water budget of Lake Pannon, conditions were more favourable for deposition of large volumes of well-developed turbidite systems during base-level rise than during stagnation or minor base-level fall. Therefore, sand delivery to the basin centre was at maximum during the early highstand aggradational stage and at minimum during the late highstand progradational stage. The timing and position of sand accumulation in the Makó Trough of Lake Pannon is different from those predicted by “traditional” sequence stratigraphic considerations.