Mediterranean inland saline lakes may play an important role in the carbon cycle due to the metabolic capacities of their prokaryotic communities. However, these lakes are not homogeneous and have different environmental characteristics. In this work, the structure and function of the prokaryotic communities inhabiting water and sediments of 15 Mediterranean inland saline shallow lakes have been studied. These lakes are grouped in categories according to their salinity, conservation statuses and alterations, which determine the structuration of the prokaryotic communities and their carbon-related metabolisms. Each salinity category and conservation status showed characteristic prokaryotic taxa. Relative abundance of methanogenic archaea tended to increase along the salinity gradient, but this did not result into increased methane emissions. The relationship between metabolic rates and the predicted abundance of their marker genes depended on the type of metabolism. Archaea played a relevant role in the organisation of interactions between community members and were markers of good conservation status. Water communities were shaped by the salinity gradient, conservation status and seasonality, while sediment communities were mostly determined by the salinity gradient. This work highlights the importance of combining molecular studies with in situ metabolic measurements to better understand carbon fluxes in inland saline aquatic ecosystems.