Four sedimentary sections were logged and sampled from upper Tortonian-lower Messinian outcrops on the island of Crete (Greece). The collected material yielded about 60 bryozoan species belonging to nine different colonial morphotypes. A few species are stenobathic, indicating either shallow- or deep-water environments, but most of them are eurybathic (with bathymetric ranges extending in some instances from the shelf down to several hundreds of metres). Bryozoan communities point to sea-level variations modulated by local tectonics. Deep circalittoral environments were recognized at the base of three sections (whereas the fourth section starts with infralittoral/shallow circalittoral environments passing to deep circalittoral. Shallow bathyal habitats follow upwards, succeeded in turn by assemblages indicative of deep circalittoral and subsequently shallow circalittoral/infralittoral depths. Inferred bathymetric fluctuations are diachronous throughout the island. Shallow-water species found associated, sometimes abundantly, with rarer deep-water faunas in a few levels, are interpreted as transported by currents. Several dysoxic episodes have been also detected: likely the result of water column stratification and enhanced productivity. These processes were probably boosted by a combination of changes in oceanic circulation, climate, global sea-level, and the local/regional tectonics (in Crete and/or the marine gateways between the Mediterranean and the Atlantic).