Rivers and the estuarine regions play crucial roles in the environment by controlling the nutrient cycling, waste disposal, and also in supporting biodiversity. However, the estuarine regions of rivers are highly susceptible to disruptive changes by anthropogenic pollutants and eutrophication. Bacterioplankton diversity is the best indicators of the pollution level and eutrophication status of the rivers. The present study evaluated the eutrophication status and bacterioplankton diversity of the estuarine regions of Chaliyar and the Anjarakkandi originated from the Western Ghats. The present study observed the presence of increased incidence of bacterioplankton comprising of proteobacteria, actinobacteria and cyanobacteria in the estuarine regions of Anjarakkandi river compared to that of Chaliyar river. Further, the percentage incidence of faecal bacteria including Bacillus subtilis and E. coli, were also found to be in high in the Anjarakkandi river; in corroborating with this, the diversity of nitrogen metabolizing bacteria was also higher in the estuarine samples of Anjarakkandi river. Corroborating with this, the levels of water nutrients including nirates, nitrites and phosphates were high in the Anjarakkandi compared to the Chaliyar river. Together, it is possible that there might be increased faecal contamination and subsequent increased eutrophication in the estuarine regions of Anjarakkandi river. Altogether, the study concludes that the Anjarakkandi river may be more polluted and which is partly contributed by faecal contaminants and also responsible for the change in the bacterioplankton community of the estuaries.