Deposits within the Caltanissetta basin of central Sicily have been important for developing the desiccating deep basin model for the Messinian salinity crisis in the Mediterranean. Linked structural and stratigraphic studies show that the Sicilian depocenters are synclines related to underlying thrust structures of the frontal part of the Maghrebian chain. Prior to the salinity crisis these basins were hydrodynamically linked through the foredeep to the Mediterranean. The precursor sediments (Terravecchia Formation) formed a delta, sourced from the north. Early Messinian regression acted on a range of paleobathymetries, shallow in the north and progressively deeper in the south, locally complicated by active thrust structures. Initial draw-down of Mediterranean base level is marked across the thrust belt by first cycle carbonates and evaporites on the structural highs and lows, respectively. Vast accumulations of halite and potassium salts (up to 1200 m) are restricted to growing thrust synclines. The different evaporite signatures may be related to different water conditions reflecting various meteoric and marine circulations across various subbasins, with cyclicity reflecting high-frequency variations in sea level. A sequence stratigraphic model is developed to explain fractionation of evaporite facies between different paleobathymetric settings and to predict the temporal evolution of the successions in different subbasins. Thrusting provides accommodation space for evaporites and also controls the water pathways into the desiccating basins. The intra-Messinian unconformity separating first and second cycle evaporites is a “type 1 sequence boundary” related to the forced regression associated with the acme of Mediterranean desiccation, an interpretation supported by local ravinement and incised valley fills. The overlying second cycle evaporites are a combination of detrital, reworked first cycle material and primary gypsum formed under brackish water. Regional onlap relationships and bed continuity suggest that this water body was of regional extent with a systematically rising base level. These interpretations have several implications for Messinian correlations in the Mediterranean: The deep basin evaporites correlate with an intra-Messinian unconformity that separates the two cycles on Sicily and postdate the first cycle deposits; regional base level was largely restored before the end of the salinity crisis.