As per title, I am wondering if is it possible to find on the web a free resource for GIS shapefiles (georeferenced) of the Mediterranean basin, or even of the whole Europe and northern Africa.
There are basin-shapefiles from Hydrosheds, you will just have to select and extract the basins (i.e. river basins) that flow into the Mediterranean. http://hydrosheds.cr.usgs.gov/index.php
I wish to thank all you colleagues for pointing out to me such interesting resources. I will check them all and I will keep you updated of any interesting finding.
Great question about data. Have you tried Open Street Map? You may have to download a lot of data by country, but you should get "official" data as well as user derived data, which may be of use :-)
For example: the data for European countries (including Malta) is at the link below:
I recommend starting with GIS Data Depot (http://data.geocomm.com/catalog/). Click on the first letter of the country you are interested in and download the free GIS files.