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We present data collected in the framework of the Algerian BAsin Circulation Unmanned Survey (ABACUS) project. The main objective of ABACUS is the monitoring of the basin circulation and of the surface and intermediate water masses' physical and biological properties in a key region of the Mediterranean Sea circulation. Data presented here have been collected through deep glider cruises in the Western Mediterranean Sea during the autumns of 2014, 2015 and 2016; activities at sea are expected to be repeated during the coming years, so that the dataset will be extended. Glider missions were conducted in the Algerian Basin, between the island of Mallorca and the Algerian coast. Across the three glider missions, eight repeated transects were completed which enabled us to investigate the basin-scale circulation and the presence of mesoscale structures, utilising both the adaptive sampling capabilities of the gliders and the higher resolution of the data. After collection, all data passed a quality control procedure and were then made available through an unrestricted repository host by the SOCIB Data Centre at 10.25704/b200-3vf5. The actual dataset spans three autumn seasons, providing an important contribution to the data collection in the chronically undersampled Algerian Basin. Temperature and salinity data collected in the first 975 m of the water column allowed us to identify the main water masses and describe their characteristics, improving the understanding of the dynamics of the region. On the timescale of the project, data show a large variability in the surface layer and reduced variability in the intermediate and deep layers. Our measurements have been successfully compared to data previously collected in the area from 1909 to 2011. Results showed similar overall distribution, ranges and variability to the historical data, with no outliers in the surface or deep layers. [ABSTRACT FROM AUTHOR]