Microbial mats, which first emerged around 3.7 billion years ago, are regarded as the earliest biological communities on Earth and are believed to have played a significant role in modulating atmospheric composition. These organosedimentary structures are organized in layers of complex microbial communities. They form through a combination of lithifying processes, such as carbonate accretion, and non-lithifying processes, where sediment is trapped by metabolites. Hypersaline lakes globally have been shown to harbor contemporary examples of these microbial mats, composed of diverse bacteria and archaea. However, what energy sources sustain them, and how communities are influenced by seasonal variation remains unclear. Here, we investigated microbial mats collected across five hypersaline lakes on Rottnest Island, Western Australia. Mats were collected with different morphology: blister, flocculent, pustular (lithifying microbial mats), cohesive, and loosely cohesive (non-lithifying microbial mats) between Jul/2015 and Mar/2016. Metagenomic analysis revealed that Pseudomonadota, Bacteroidota, Cyanobacteriota, Chloroflexota, and Halobacteriota are the most dominant groups. Functional profiling showed that communities are primarily composed of organoheterotrophs that harbor the potential for inorganic energy acquisition from sulfide, as well as aerobic hydrogen and carbon monoxide metabolism oxidation. Additionally, genes supporting photosynthesis and nitrogen fixation were highly enriched, suggesting a key role of these processes in microbial mat formation. Mat morphology and seasonal effects were also found to play a significant role as determinants of these functional genes. Our findings suggest that microbial mat formation in hypersaline lakes is driven by a combination of organic and inorganic energy sources such as sulfide and trace gases, which are significantly modulated by seasonality and mat morphology. Our findings provide functional insights into the complex biogeochemical processes governing these ancient structures' formation and ecosystem services, providing a basis for their conservation and protection from threats such as pollution and anthropogenic disturbance.