Peat bogs have an important role in the carbon cycle, as they may be sinks or sources of carbon dioxide and methane, depending on the environmental conditions. These wetlands represent large reservoirs of freshwater capable of mitigating drought-flood events, with important implications for water quality and hydrological balance. The key nature contributions to people provided by these ecosystems are tightly related with the diversity of microbial communities inhabiting them. Peat bogs from Tierra del Fuego Island usually host several water bodies embedded within a waterlogged Sphagnum matrix. These aquatic habitats can be considered as extreme environments due to their low pH values and dystrophic conditions and show a uniquely adapted biota. In this chapter, we unravel the diversity of the aquatic algae, ciliate and microinvertebrate communities from two peat bogs from Tierra del Fuego at different scales. For the different communities analysed, we identified distinct diversity patterns relating to local environmental conditions, as well as taxa of high value as indicators of the possible impact on peat bog diversity exerted by anthropogenic activities in a global change context.