Data on an experiment to find out the interconnections between soil physicochemical properties and the microbial communities residing in the topsoil and the subsoil of irrigated orchards under a semiarid Mediterranean climate. We collected soil samples from two depths, topsoil (0-10 cm) and subsoil (30-50 cm), noting elevated salinity levels in the topsoil due to irrigation practices. Utilizing high-throughput 16S rRNA gene and ITS1 region amplicon sequencing, we characterized the bacterial and fungal communities across these two depths.