This data package includes the abundance of microbial operational taxonomic units (OTUs) for samples collected during the austral summer of 2012-2013 in the Lake Hoare and Goldman Glacier Basins of Taylor Valley, Antarctica. A total of twenty samples from on- and off-water track soils were collected and analyzed. Samples were collected from the Lake Hoare Basin on 27 December 2012 and from the Goldman Glacier Basin on 4 January 2013. The aim of the study was to identify how variation in the measured physical and chemical environment of water tracks within the two water track systems influenced soil microbial community structure and diversity. Soil bacterial biodiversity was assessed using cultivation independent 16S rRNA gene sequencing.