The Mediterranean Sea, as a “centre” of the ancient world, has been early recognized as a laboratory basin for a variety of atmospheric, ocean and climate studies. Its uniqueness is manifested in its geographical position, a mid-latitude region connecting three continents, orography that affects cyclogenesis, precipitation and winds, ocean bathymetry that is shaped by narrow and shallow straits, passages and sills, and other. Its both atmospheric and oceanic climate is distinctive and, while differing substantially from neighbouring continents and oceans, it strongly interferes and shapes their properties. One of such adjacent basins is the Black Sea, which is, albeit minor in quantity, providing a noteworthy impact to the Mediterranean and vice versa. This topical volume of Pure and Applied Geophysics is presenting recent investigations of atmospheric and ocean properties, processes and climate of both basins, being inspired by presentations given in the Joint Congress of the 6th International Conference on Meteorology and Climatology of the Mediterranean & Challenges in Meteorology 5, held in Zagreb, Croatia, on 20-22 February 2017. The volume comprises 22 papers that are classified in three research categories: (1) storms, extremes and mesoscale processes, (2) atmospheric climate, variability and climate change, and (3) ocean climate and variability. The papers investigate processes occurring over a variety of spatial and temporal scales, from hemispheric processes that drive the observed changes in the Mediterranean and Black Sea, through phenomena that are influencing the whole basin or its sub-basins, to local and mesoscale extreme events that are affecting large cities and local populations in the region. The volume is of interest to atmospheric and oceanic researchers involved in a variety of processes that are occurring over the Mediterranean and Black Sea region. This particularly refers to young researchers and PhD students that are yet to enter to research of this unique and exciting region full of challenges that need an interdisciplinary, innovative and state-of-the-art approaches in solving actual research problems.