The drainage and ammonium leachate of rare earth elements (REEs) mining activities has brought severe environmental acidification and high concentration of REEs and saline to the surrounding river. In previous 16S rRNA analyzing result, pH was showed as the major factor affecting microbial structure, followed by saline and REEs. Furthermore, microbial phylogenetic analysis identified Archaea represent a significant fraction (up to 45.5%) of total prokaryotic community under high-polluted condition. Yet, Archaea remain much less well understood than Bacteria in terrestrial habitat. To this end, we applied genome-resolved metagenomics analyses to provide initial molecular insights into the ecological role of these lesser known, but potentially important, Archaea in the contaminated river environment. We sequenced DNA from complex sediment and planktonic consortia from river adjacent to Dingnan REEs tailings in South China, successfully obtained 19 archaeal draft genomes belonging to two major group: Thaumarchaeota, and small acidophilic archaea affiliated with Micrarchaeota phyla. Genome analysis indicated these archaea appear to be capable of denitrification, dissimilatory nitrate reduction to nitric oxide, ammonia oxidation. Interestingly, they also have sulfate reduction/oxidation genes suggesting they have an important role in intermediate sulfur cycling. These study expands our knowledge of ecological roles of these mesophilic archaea, and reveal their involvement in carbon, nitrogen, and sulfur cycling in contaminated river on genomic scale. This work was supported by the National Key R&D Program of China (2018YFD0800700), and the 111 Project(B18060).