The northeastern regions of Algeria are known for their abundance of hot springs. These hydrothermal sites offer an opportunity to explore their microbial ecology and biotechnological potential. Of the 240 existing hot springs, only a few have been studied for microbial biodiversity. The selected hot spring is located in N’Gaous in the city of Batna, in eastern Algeria. This study focuses on the analysis of the physicochemical parameters of the hot spring water and aims to investigate and compare the abundance and diversity of the associated microbial community using a culture-independent approach—next-generation sequencing (Illumina, MiSeq), as well as to identify the most relevant environmental factors influencing changes in community diversity at different spatial scales. Metagenomic sequencing data revealed the predominance of Bacteria over Archaea. The most abundant phyla in the Saïda hot spring are the Proteobacteria. A differential abundance of microbial species belonging to the phyla Proteobacteria, Firmicutes, Chloroflexi, and Deinococcus-Thermus was also detected. Piper’s diagram classifies the Saïda hot spring water as belonging to the Na-SO₄ chemical facies. The physicochemical parameters of the water comply with WHO guidelines. Environmental factors like temperature and ion concentrations influence microbial community composition at this geothermal site. Additionally, the presence of several unclassified bacteria and archaea suggests a complex physiological system that requires further investigation.