Calcareous nannoplankton population underwent a major reorganization across the early and middle Eocene. This reorganization was mainly explored from an open ocean perspective, but marginal settings are usually underexplored. Here we analyzed a Tethyan pelagic record from Avdat, southern Israel in the Levant margin. The calcareous nannofossil assembledge was then compared to a number of Deep Sea and Ocean Drilling sites through paleoecological techniques. From calcareous nannofossil zone NP12 until zone NP15-16 (undiff.), dominance shifted from to discoasters in the warm early Eocene, and then to responding to cooling in the middle Eocene. Markers for middle Eocene oceanic destratification and mixing, e.g., the acme, peak and the first occurrence of , are delayed by ~1.0 Myr at Avdat with respect to oceanic sites at comparable paleolatitudes, and more so when compared to higher latitude sites. The Avdat section is punctuated by peaks of , diversity of spp., and that were not reported in deep oceanic sites. The disparities at Avdat vs. other oceanic localities can be ascribed to its position in a Tethyan remnant ocean surrounded by land masses and orogenic terrains. The punctuational mode and delay in water destratification in the Levant ocean are attributed to connection to warm and saline water off the Afro-Arabian shelf affected by pulses of cooler waters from Boreotropical marine connections, and sea level fall late in the Middle Eocene, increasing proximity to shelves.