Organic-walled palynomorph assemblages from the Kasterlee Formation in northern Belgium provide new insights into the Late Miocene depositional history and palaeoenvironments of the southernmost North Sea Basin. Ranges of key dinoflagellate cysts constrain the unit between 7.5 and 5.32 Ma, that is, a latest Tortonian to Messinian age. The palynomorph assemblage is characterized, amongst others, by Geonettia clineae, an opportunistic species that thrives in mesotrophic, coastal embayments with a low sediment influx. This environmental setting is corroborated by the notable presence of Gramocysta verricula, a species with preference for shallow marine environments. The occurrence of species of the fresh water green alga Pediastrum indicates manifest river discharge in a near-shore environment or embayment. The coastal depositional environment mirrored by the palynomorphs of the Kasterlee Formation succeeds the distinct transgressive and fully marine environments of the underlying Diest Formation in the Campine area. The results from the palynological study, combined with lithological and geophysical data, show that both Upper Miocene formations are two distinct depositional cycles separated by an erosional or regressive phase. The upper boundary of the Kasterlee Formation is correlated with the Me2 sequence boundary at 5.73 Ma. The Kasterlee Formation is herein formally moved from the Lower Pliocene series to the Upper Miocene series. The coastal environment, probably characterized by a shoaling phase, recorded at the border of the southern North Sea Basin, matches the global record of regressive phases in Messinian sedimentary sequences, which are linked to cooling and increasing global ice volume.