A summer survey was conducted on the bacterioplankton communities of seven lakes from Byers Peninsula (Maritime Antarctica), differing in trophic and morphological characteristics. Predictions of the metabolic capabilities of these communities were performed with FAPROTAX using 16S rRNA sequencing data. The versatility for metabolizing carbon sources was also assessed in three of the lakes using Biolog Ecoplates. Relevant differences among lakes and within lake depths were observed. A total of 23 metabolic activities associated to the main biogeochemical cycles were foreseen, namely, carbon (11), nitrogen (4), sulfur (5), iron (2), and hydrogen (1). The aerobic metabolisms dominated, although anaerobic respiration was also relevant near the lakes’ bottom as well as in shallow eutrophic lakes with higher nutrient and organic matter contents. Capacity for using carbon sources further than those derived from the fresh autochthonous primary production was detected. Clustering of the lakes based on metabolic capabilities of their microbial communities was determined by their trophic status, with functional diversity increasing with trophic status. Data were also examined using a co-occurrence network approach, indicating that the lakes and their catchments have to be perceived as connected and interacting macrosystems, where either stochastic or deterministic mechanisms for the assembling of communities may occur depending on the lake’s isolation. The hydrological processes within catchments and the potential metabolic plasticity of these biological communities must be considered for future climate scenarios in the region, which may extend the growing season and increase biomass circulation.