The main island of New Caledonia (NC) is surrounded by the second largest barrier reef in the world after the Australian Great Barrier Reef. The Upper Pleistocene evolution of this barrier reef–lagoon complex offers the opportunity to examine the response of a modern mixed tropical siliciclastic/carbonate system to relative sea-level changes and to better constrain the relative role of lagoon backfilling and paleo-drainage system in sediment transfer across the shelf. This paper mainly focuses on the results of chronostratigraphic and sedimentological interpretations of new seismic, bathymetric and coring data collected in the SW NC lagoon. Several significant points are highlighted from this study and allow the construction of a refined model which includes the evolution of both the SW NC mixed shelf and lagoon. New results show that the NC lagoon has not recorded a reciprocal sedimentation during glacial-interglacial sea-level cycles but a unique mixed regime. Strong contrasts are observed and these depend above all on the two lagoon domains: the outer coral plateau and the inner lagoon depression corresponding to a semi-closed proximal basin which is separated from the plateau by a basement ridge. In the depression, clastic sediments remain dominant from early flooding to highstand stages while carbonate sedimentation continued through time across the coral plateau. This spatial contrast between terrigenous and carbonate deposits was maintained throughout various sea level cycles. Thus, even if spatial segregation is also observed for other examples of mixed shelf environments, the SW NC shelf appears quite unique in comparison to the other mixed systems when considering conceptual models of reciprocal sedimentation. Moreover, the presence of a semi-enclosed lagoon depression allows the preservation of larger volume of terrigenous deposits. This semi-filled geometry of the lagoon is assumed to be the result of several factors: a significant subsidence that offers accommodation for aggrading deposits, evacuation through channels of sediments mobilized during storm events, the tidal currents, and fairweather wave dynamics. Lastly, the inherited morphologic and structures may explain the geomorphic evolution of the “escarpment margin” type of the SW NC rimmed shelf and its differentiation with the opposite SE NC ramp type shelf.