Culturable bacterial diversity and co-occurrence of heavy metal and antibiotic resistance were investigated from the water and sediments along the course of the Teesta River, in the Eastern Himalayas. Water and sediment samples collected from six sampling points during the monsoon and winter seasons were subjected to analysis of physico-chemical parameters, heavy metal contamination and antibiotic tolerance. The culturable bacterial diversity established by application of bacterial culture and 16S rRNA gene sequencing, ascertained the majority belonged to Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Deinococcus-Thermus. Among the 5 phyla, Proteobacteria and Actinobacteria were the dominant phyla present in both water and sediment samples, whereas Bacteroidetes, Firmicutes and Deinococcus-Thermus were unique to particular sites. The Shannon index indicated that the bacterial richness was more in the water column as compared to sediment. From the total of 245 isolates, 69 genera were identified. Heavy metal tolerance and antibiotic resistance profiles showed some isolates to be tolerant to high levels of heavy metals and multiple antibiotics indicating a major concern in terms of river ecosystem serving as a pool for dissemination of such resistant genes. The antibiotic resistance and heavy metal contamination diversified along the human-impacted downstream sites, endorsing the contribution of anthropogenic factors. The present report on bacterial diversity and the associated metal and antibiotics tolerance among bacteria is the first of its kind on Teesta River, the only major river system flowing through the state of Sikkim and parts of North Bengal.