In many highly urbanized areas, effluent from wastewater treatment plants (WWTPs) represents a significant proportion of the water source for receiving rivers. Microbial communities are major components of riverine ecosystems and mediate the processes of nutrients and organic matter produced by treated and untreated WWTP effluent. To date, the impacts of WWTP effluent discharge on riverine microbial communities remain poorly understood. Based on 16S rRNA gene sequencing and water quality analysis, we investigated the microbial community compositions and predicted functions in the effluents of five municipal WWTPs and their receiving rivers. The results showed that the microbial compositions in the five WWTP effluents with different treatment processes were similar. Significant differences in the microbial community were not noted between the effluent, upstream, and downstream sites for both sampling months. However, dissimilarity of microbial composition between two sampling periods was observed. The temperature, pH, dissolved oxygen, and ammonium were major environmental factors associated with microbial community changes. Functional annotations of microbial communities based on 16S amplicons identified xenobiotic degradation and metabolism functions in effluent and river samples. Quantitative polymerase chain reaction revealed the dominance of ammonia-oxidizing bacteria (AOB) over ammonia-oxidizing archaea (AOA) in the WWTP effluents and rivers, and significant positive correlation between AOB abundance and nitrate concentration was observed. These findings will help increase our understanding of the impact of effluent discharge on urban river ecosystems.