Septic tanks (STs), up-flow anaerobic filters (UAFs), and horizontal-flow constructed wetlands (HFCWs) are cost-effective wastewater treatment technologies especially efficient in tropical and sub-tropical regions. In this study, the bacterial communities within a decentralized wastewater treatment plant (WWTP) comprising a ST, a UAF, and a HFCW were analyzed using high-throughput sequencing of the V3–V4 region of the 16S rRNA gene. Bacterial diversity and its spatial variation were analyzed at the phylum and family level, and principal component analysis (PCA) was applied to nitrogen- and organic-matter-degrading families. The highest percentage of nitrogen removal was seen in the HFCW (28% of total Kjeldahl nitrogen, TKN, and 31% of NH3-N), and our results suggest that families such as Rhodocyclaceae (denitrifying bacteria), Nitrospiraceae (nitrifying bacteria), and Rhodospirillaceae (sulfur-oxidizing bacteria) contribute to such removal. The highest percentage of organic matter removal was seen in the UAF unit (40% of biological oxygen demand, BOD5, and 37% of chemical oxygen demand, COD), where organic-matter-degrading bacteria such as the Ruminococcaceae, Clostridiaceae, Lachnospiraceae, and Syntrophaceae families were identified. Redundancy analysis demonstrated that bacterial communities in the HFCW were more tolerant to physicochemical changes, while those in the ST and the UAF were highly influenced by dissolved oxygen and temperature. Also, pollutant removal pathways carried out by specific bacterial families and microbial interactions were elucidated. This study provides a detailed description of the bacterial communities present in a decentralized WWTP located in a subtropical region.