Quantitative analysis of 67 calcareous nannofossil assemblages from surface sediments recovered in a wide area across the Sicily Channel has been carried out in order to improve the interpretation of palaeontological data based on this planktonic group in a key area for Mediterranean palaeoceanographic studies. The investigation focused on three case studies that demonstrate the high potentiality of such a combined approach, taking into account the recent distribution of taxa or groups of taxa on the sea floor and the palaeontological record. The distribution of reworked specimens over the northern Sicily Channel sea floor validates the role of southern Sicily as a source region for reworked nannofossils and the role of rivers as their carrier. Eustatic sea-level fluctuations can be considered to be the main factor that influenced the abundance variations in sedimentary sequences of this area. The distribution of Florisphaera profunda can be explained in terms of topography (positive correlation) and mesoscale oceanographic circulation. In particular, its significant anti-correlation to the amount of chlorophyll-A deduced by satellite imagery validates the use of this species as a proxy for palaeoproductivity reconstructions. Finally, high abundance values of G. oceanica are confined to the westernmost part of the Sicily Channel, coinciding with a water mass salinity minimum. In particular, abundances of up to about 10% were observed in the westernmost part of the African Margin, suggesting the importance of the Atlantic Tunisian Current, whose activity is more pronounced in winter. The comparison of data of this species between 135 and 110 kyr BP, inside and outside the Channel, led us to deduce that the physical transport in almost unmodified waters of Atlantic origin might be the most important factor for its significant occurrence.