Results from a recent hydrographic survey show that an influx of Aegean Sea water has replaced 20 percent of the deep and bottom waters of the eastern Mediterranean. Previously, the only source of such waters was the Adriatic Sea, and the waters of the eastern Mediterranean were in near-steady state. The flux changed the water characteristics and displaced older waters upward. Its cause was increasing Aegean Sea salinity, resulting from changes in either the circulation pattern or the large-scale freshwater balance. Current deepwater studies may be affected by the intrusion, but effects might be found also at shallower depths and over a larger region.

This paper is the outcome of a workshop held in Rome in November 2011 on the occasion of the 25th anniversary of the POEM (Physical Oceanography of the Eastern Mediterranean) program. In the workshop discussions, a number of unresolved issues were identified for the physical and biogeochemical properties of the Mediterranean Sea as a whole, i.e., comprising the Western and Eastern sub-basins. Over the successive two years, the related ideas were discussed among the group of scientists who participated in the workshop and who have contributed to the writing of this paper. Three major topics were identified, each of them being the object of a section divided into a number of different sub-sections, each addressing a specific physical, chemical or biological issue: 1. Assessment of basin-wide physical/biochemical properties, of their variability and interactions. 2. Relative importance of external forcing functions (wind stress, heat/moisture fluxes, forcing through straits) vs. internal variability. 3. Shelf/deep sea interactions and exchanges of physical/biogeochemical properties and how they affect the sub-basin circulation and property distribution. Furthermore, a number of unresolved scientific/methodological issues were also identified and are reported in each sub-section after a short discussion of the present knowledge. They represent the collegial consensus of the scientists contributing to the paper. Naturally, the unresolved issues presented here constitute the choice of the authors and therefore they may not be exhaustive and/or complete. The overall goal is to stimulate a broader interdisciplinary discussion among the scientists of the Mediterranean oceanographic community, leading to enhanced collaborative efforts and exciting future discoveries.

Adriatic and Ionian seas are Mediterranean sub-basins linked through the Bimodal Oscillating System mechanism responsible for decadal reversals of the Ionian basin-wide circulation. Altimetric maps showed that the last cyclonic mode started in 2011 but unexpectedly in 2012 reversed to anticyclonic. We related this "premature" inversion to the extremely strong winter in 2012, which caused the formation of very dense Adriatic waters, flooding Ionian flanks in May and inverting the bottom pressure gradient. Using Lagrangian float measurements, the linear regression between the sea surface height and three isopycnal depths suggests that the southward deep-layer flow coincided with the surface northward geostrophic current and the anticyclonic circulation regime. Density variations at depth in the northwestern Ionian revealed the arrival of Adriatic dense waters in May and maximum density in September. Comparison between the sea level height in the northwestern Ionian and in the basin centre showed that in coincidence with the arrival of the newly formed Adriatic dense waters the sea level was lowered in the northwestern flank, inverting the surface pressure gradient. Toward the end of 2012, the density gradient between the basin flanks and its centre went to zero, coinciding with the weakening of the anticyclonic circulation and eventually with its return to the cyclonic pattern. Thus, the premature and transient reversal of Ionian surface circulation originated from the extremely harsh winter in the Adriatic, resulting in the formation and spreading of highly dense bottom waters. The present study highlights the remarkable sensitiveness of the Adriatic–Ionian BiOS to climatic forcing.

In winter 1995 the last major field work of the Physical Oceanography of the Eastern Mediterranean (POEM) program was carried out, the Levantine Intermediate Water Experiment (LIWEX). In this study a thorough analysis is presented of the data set collected during three successive surveys in January, February, and March–April 1995. The major overall result is that the Levantine basin is shown to be the site for multiple, and different, water mass formation processes. Levantine Deep Water (LDW) was formed in the Rhodes gyre, with the preconditioning phase starting in December 1994. In late January the chimney was ventilating to the atmosphere. In February the strong mixing phase is documented by the convective cell vertically homogeneous to 900 m depth. In March–April, recapping has occurred in the upper 200 m. LDW remained confined inside the Rhodes gyre cyclonic circulation. Levantine Intermediate Water (LIW) is instead deeply affected by the upper thermocline circulation. Shallow ventilating chimneys with the LIW thermostads were found in the January survey inside the cyclonic region of the northern Levantine. The formation process of LIW does not involve deep penetrative convection. Winter surface cooling and evaporation are sufficient to produce a surface mixed layer 100 m deep with LIW characteristics. At the mixed layer basis, LIW subducts and spreads along isopycnal surfaces along pathways determined by the cyclonic/anticyclonic structures of the upper thermocline circulation.