This work is a description of the water masses and circulation in the site of the CINCS (Pelagic–Benthic Coupling IN the Oligotrophic Cretan Sea) experiment in the southern boundary of the Cretan Sea, a region of recently renewed interest with respect to the hydrology of the Eastern Mediterranean Basin. Analysis of hydrological data from the study area reveals the presence of five water masses: local surface water and remotely advected Modified Atlantic Water (MAW) share the surface layers below them are Cretan Intermediate Water (CIW), between 50 and 150 dbar, Transition Mediterranean Waters (TMW) with its core located between 300–400 dbar, and the Cretan Deep Waters (CDW) occupying the depths below 800 dbar. The circulation over the coastal shelf and slope is dictated by the offshore semi-permanent mesoscale features that dominated the Cretan Sea in 1994–1995, forcing locally a shoreward flow. The hydrographic observations are verified by current-meter measurements from a mooring in the sampling area. The recorded velocity is generally towards the SE direction, seasonally modulated, reaching maximum speeds of 27 cm s−1. Analysis of the new data set has revealed a previously unobserved feature of the oceanographic characteristics of the region. Over the base of the Cretan Slope there occur lenses of water that are warmer and more saline than their surroundings. These lenses probably form on the shelf seasonally; their waters are rich in oxygen, and have a density that is higher than historical Cretan Deep Water values.

The Cretan Basin can be characterized as a back-arc basin of the Hellenic Trench System, that is related to the subduction zone of the African Plate under the Eurasia Plate. The study area includes the narrow and relatively steep (gradient 1.5°) continental shelf of the island of Crete followed by the steep slope (2°–4°) and the rather flat deeper part of the Cretan basin (water depths >1700 m). Surficial sediments of the coastal zone are coarser and of terrigenous origin, while in deeper waters finer sediments, of biogenic origin, are more abundant. Sand-sized calcareous sediment accumulations, identified in middle-lower slope, may be attributed to the aggregation of seabed biogenic material related to the near bed current activity. High resolution profiles (3.5 kHz) taken from the inner shelf shows a typical sigmoid-oblique progradational configuration, implying prodelta sediment accumulation during the Holocene. In the upper-middle slope, sub-bottom reflectors indicate continuous sedimentation of alternating fine and/or coarse grained material. Small-scale gravity induced synsedimentary faults appeared, locally. In contrast, a series of gravity induced faults, identified in the lower slope, are associated with sediment instabilities due to seismotectonic activity. Sediment cores taken from the shelf-break consists of calcareous muddy sand with small amounts of terrigenous silt and fine sand, while the cores recovered from the middle slope has revealed a more homogeneous fine sediment texture of hemipelagic deposition. The prevailing accumulation processes in the southern margin of the Cretan basin are: (i) prodelta deposition in the inner-middle shelf; (ii) settling from bottom nepheloid layers in the shelf and upper slope; (iii) calcareous sediment formation due to settling from suspension and post accumulation aggregation (middle-lower slope); (iv) long-term episodic sediment gravity processes in the lower slope; and (v) to a lesser extent, redeposition from resuspension due to gravity processes and bottom currents.