Cenozoic carbonate platforms in the central Mediterranean region show distinct vertical changes in carbonate skeletal assemblages and porosity characteristics that reflect shifts in environmental conditions affecting the western Tethys. The Photozoan Association produced by carbonate ecosystems adapted to low nutrient environments and the Heterozoan Association favoured by mesotrophic conditions alternate through time over the Malta Platform and nearby carbonate platforms, although not in phase with trans-Mediterranean Oligocene carbonates. This anomaly reflects the transitional nature of Cenozoic climate as well as continental convergence of the Tethyan margins. Restricted conditions amplified the effect of nutrient flux from North African fluvial systems, which was controlled by meridional shifts in the inter-tropical convergence zone (ITCZ) precipitation belt. We model the climate–carbonate interaction by comparing the global oxygen isotope proxy to ice volume and meridional position of the ITCZ to changes in trophic level of carbonate ecosystems. The results show that the development of Palaeogene Mediterranean photozoan assemblages coincides with periods when the ITCZ had shifted away from North Africa (as is the case presently), whereas the heterozoan assemblages thrived during increased nutrient flux when the precipitation belt was located over the Sahara. The climatic controls resulted in facies characteristics that exert a fundamental influence on porosity in carbonate reservoirs.