In this work the ability of nesting two hydrodynamical models, the high-resolution Cretan Sea shelf model and the lower resolution regional ALERMO model, was investigated. A new database was developed by objectively analysing raw climatological data from the MODB database enriched with in situ measurements collected by the Institute of Marine Biology of Crete. Prior to nesting with the ALERMO model, the Cretan Sea model was integrated using this new hydrological database, in order to investigate the capability of the model setup to describe the phenomenology of the Cretan Sea. Results show that the model can successfully reproduce the complex general circulation characteristics of the area, such as the dipole of a cyclone and an anticyclone, and the flow reversal between winter and summer. As a next step, the shelf-model was one-way nested with the ALERMO model and was integrated on a climatological basis. The evolution of the circulation characteristics of the Cretan Sea was compared, qualitatively and quantitatively, against the results of the regional model, and proved that the nesting between the two models can provide reliable information while overcoming at the same time the computational constraints imposed by high-resolution models