The Dead Sea is characterized by a very low density of cells most of which are Archaea. We discovered several systems of underwater fresh to brackish water springs in the Dead Sea, often located at depths that did not allow detection from the shore. We explored one such system and found dense microbial communities. In this study we provide the first characterization of these communities and discuss possible sources of these organisms, their hydrochemical environment, energetic resources and the putative biogeochemical pathways they are mediating. Pyrosequencing of the 16S rRNA gene and fingerprinting methods showed that the spring community originates from the Dead Sea Group sediments and not from the spring water-borne community. Furthermore, it suggested that there is a large Archaeal community in the shoreline pore water of the lake. Sequences of bacterial sulfate reducers, nitrifieres iron oxidizers and iron reducers were identified as well. Analysis of green and white biofilms suggest that sulfide oxidation through chemolitotrophy and phototrophy is highly significant. Hyperspectral analysis additionally showed a tight association between abundant green sulfur bacteria and cyanobacteria in the green biofilms. Together, our findings show that the Dead Sea floor harbors diverse microbial communities, part of which is not known from other hypersaline environments. The underwater springs are a newly recognized water source for the Dead Sea. Their input of microorganisms and nutrients needs to be considered in the assessment of possible impact of dilution events of the lake surface waters, such as those that will occur in the future due to the intended establishment of the Red SeaDead Sea water conduit.