© 2017 Elsevier B.V. 231Pa, 230Th and 232Th were analyzed in unfiltered seawater samples (n = 66) and suspended particles (n = 19) collected in the Mediterranean Sea during the MedSeA-GA04-S cruise along the GEOTRACES section GA04S and used to investigate mechanisms controlling the distribution and fractionation of Pa and Th in an ocean margin environment. 231Pa and 230Th are particle reactive radionuclides and are often used as tracers of processes such as boundary scavenging, particle transport and ocean circulation. The depth profiles of total 231Pa and 230Th concentrations in the Mediterranean Sea displayed non-linear shapes. Higher total 232Th concentrations were observed at the straits and in deep waters pointing at lithogenic sources. Fractionation factors FTh/Pa ranged from 1.4 to 9. Application of a box-model illustrated that 94% of the 231Pa and almost all of the 230Th (99.9%) produced in the Mediterranean Sea is removed to the sediment by scavenging. The negligible export of 230Th to the Atlantic Ocean, leads to a reevaluation of the mean settling speed of the filtered particles, which is now estimated to 500–1000 m/y. The low FTh/Pa fractionation factors are attributed to the efficient scavenging and lack of transport of 231Pa to the Atlantic Ocean.