We present an assessment of the water mass dynamics in a reanalysis of the Mediterranean Sea with a focus on the Algero‐Provencal basin. We use a θ‐S‐based algorithm to compute the fractions of the main western Mediterranean water masses: Atlantic and modified Atlantic Waters (AW and mAW), Western and Eastern Intermediate Waters (WIW and EIW), Tyrrhenian and Western Mediterranean Deep Water (TDW and WMDW). The reanalysis retains the known mean characteristics of the water masses, their seasonal to interannual variabilities, and main circulation patterns when compared with the literature. The imprint of winter mixing is particularly obvious with coherent variations of water mass volumes, mainly the yearly creation of WIW from mAW on northernmost shelves and of WMDW from all surface and intermediate layers during years of deep water formation (DWF). The results also highlight some unrealistic events of variability of the WMDW volume that are likely due to the data assimilation process. Recomputation of water mass volumes and transports without these altered years allowed to highlight the possible disruption of large‐scale barotropic cyclonic circulation in the East Algerian basin in response to major DWF events over the Gulf of Lion and the induced surface consequence on Algerian Eddies' trajectories.