The Eastern Mediterranean Sea (EMS) is an ultraoligotrophic semi-enclosed sea with low nutrient levels, low primary production rate, impoverished phytoplankton populations and low zooplankton standing stocks. The Cretan Passage in the western Levantine Sea is one of the least explored areas of the EMS. We measured the mesozooplankton biomass, abundance and taxon composition as well as biochemical parameters like Εlectron Τransport System (ETS) activity and Aminoacyl-tRNA Synthetases (AARS) activities in late spring of 2016 (28 March–17 April 2016). The sampling area is influenced by the presence of the permanent Rhodes Cyclonic Gyre east of Crete and a series of smaller permanent or recurrent gyres south of Crete which influence the pathway of the Atlantic Water from the Ionian Sea towards the Levantine Basin at surface and subsurface layers. Mesozooplankton abundance showed slightly increasing values from western to eastern stations of the Cretan Passage and although subsurface maxima were recorded in the 50–100 m layer, the abundance at all stations generally decreased with depth. The community was dominated by copepods at all stations. Juveniles of Clausocalanus followed by juveniles of Oithona and the Oncaea media group (Oncaea waldemari, Oncaea scottodicarloi, Oncaea media) were the most abundant taxa in the upper layer, whereas Mormonilla minor, Haloptilus longicornis and Subeucalanus monachus were mainly found below 100 m. ETS, AARS and biomass for carbon measurements were conducted in the same area for the 0–100 m and 0–500 m layers. ETS was highest at LV13 with 10.56 ± 1.33 μl O2 h−1 mg protein−1 in 0–500 m and carbon biomass was highest at LV18 with 4.99 mg m−3 in 0–100 m. Lowest values of 4.52 ± 1.46 μl O2 h−1 mg protein−1 at LV18 in 0–100 m were detected for ETS and 0.91 mg m−3 at LV10 in 0–500 m for carbon biomass. Specific AARS activities showed no significant differences among sites. On the basis of ETS and AARS, we calculated that the zooplankton carbon requirements follow the west to east trend of zooplankton biomass, however, the zooplankton is not well fed and the organisms are living under oligotrophic stress.