High anthropogenic N loads and abundant bacteria are characteristic of highly contaminated urban rivers. To better understand the dispersal and accumulation of bacteria, we determined contents and isotopic compositions of suspended particulate organic matter (SPOM) and bacteria in a highly contaminated urban river (the Nanming) and effluents in winter and summer of 2013. Relative to SPOM, bacterial biomass in the river was depleted in ¹³C and ¹⁵N and its C/N ratio was lower (δ¹³C: − 33.2‰ ± 3.1‰; δ¹⁵N: − 1.5‰ ± 1.2‰; C/N: 4.8 ± 0.6), while effluents showed higher ¹³C and ¹⁵N contents and C/N ratios (δ¹³C: − 25‰ ± 2.1‰; δ¹⁵N: + 8.5‰ ± 1.1‰; C/N: 8.1 ± 1.2). Source recognition of SPOM was based on carbon isotopes because they are conservative and distinct between end-members (effluent detritus and bacterial biomass). Using a mixing model, bacterial biomass in the river was calculated to account for < 20% and < 56% of bulk suspended particulate organic nitrogen in winter and summer, respectively. An N budget showed that bacterial N was a small proportion of total nitrogen (< 7.4%) in the riverwater.