Hydrological decadal trends of Mediterranean waters (MWs, e.g., salinification of ∼0.01/decade) have been imputed to local environmental changes, hence assuming unchanged inflowing Atlantic water (AW), which is an unchecked hypothesis. To better understand the long-term changes in the sea, an autonomous CTD has been moored, among others, on the Moroccan shelf in the strait of Gibraltar. We show that the inflowing AW salinity displays a marked seasonal variability, due to mixing conditions, and a huge interannual variability, having continuously increased by ∼0.05/year in 2003–2007; the AW yearly trend is dozens times larger than the MWs decadal one. The ∼0.20 overall salinification being associated with a ∼0.12 kg/m3 densification, reliable data analyses and numerical models dealing with the sea functioning must definitely consider the interannual variability of the inflow. Autonomous CTDs are efficient instruments and the variance criterion is a valuable data selection technique.