Antarctic meltwater ponds are an abundant, dynamic and sensitive yet poorly understood ecosystem. In this thesis, bacterial communities from surface waters, the water column and benthic zone in geochemically variable meltwater ponds in the Ross Sea Region of Antarctica were investigated. The primary objective of this research was to provide a detailed description of the community composition and to determine the temporal, geochemical and geomorphological drivers of community structure. A coordinated comparable analysis method was used for all samples so that, although separated into the previously mentioned zones, findings could be directly compared across studies. Bacterial community structure between samples was initially investigated by Automated Ribosomal Intergenic Spacer Analysis (ARISA) of the 16S rRNA gene which, combined with in-situ collected geochemistry data was used to identify trends requiring high throughput sequencing (454 pyrosequencing of the V5-V6 hypervariable region of the 16S rRNA gene) analysis coupled with nutrient and elemental data. A preliminary study in December 2009 compared the water columns of five geochemically distinct ponds. Communities between ponds were distinct, their structure driven primarily by pH and conductivity. One geochemically stratified pond formed distinct surface and bottom clusters with increasing diversity and changes to phyla structure with depth. Temporal and geomorphological (Bratina Island and Miers Valley) drivers of variation in the microbial community structure between the surface waters of 41 ponds were examined. Conductivity was identified as the most significant driver across all ponds for the dominant cosmopolitan community, however trace elements were more significant drivers of community structure for the unique community (those sequences absent in at least one pond). Pronounced variation was identified between December and January samples and although the bacterial components of the community were similar between January 2012 and 2013 the community structure varied significantly. Despite different environments, communities from the Miers Valley were not well differentiated from Bratina Island, suggesting biological exchange between locations. The stratified water column of six Bratina Island and two Miers Valley ponds was investigated. Strongly geochemically stratified ponds exhibited a heterogeneous vertical community structure related to conductivity and dissolved oxygen. Variation in community structure was primarily driven by the abundance of a small number of cosmopolitan OTUs that changed with depth. Although the biological constituents were the same, minor variation in community structure was identified within Huey pond between years (2012 and 2013). Variation between Huey pond (Bratina Island) and Morepork pond (Miers Valley) was correlated with variation of iron and mercury concentration. Lastly the benthic zone of six ponds from Bratina Island and six from the Miers Valley was examined. The community structure was highly heterogeneous and diverse with 21 phyla identified. No distinction was identified between the two locations with the majority of pyrosequencing reads shared. Potassium, sodium and cobalt were identified as the most significant explanatory variables to the cosmopolitan community and aluminium, uranium and magnesium to the unique community. This study has granted an unprecedented understanding of the bacterial communities in the meltwater ponds of the Ross Sea Region. Geochemical inter pond heterogeneity is matched with an equally heterogeneous bacterial communities, primarily driven by conductivity. Although harboring a complex and diverse community the majority is comprised of a small number of shared OTUs across spatial and temporal scales.