Abstract In aquatic ecosystems, real-time water-quality (WQ) biomonitoring has become the most effective technology for monitoring toxic events by using living organisms as a biosensor. In this study, an online WQ monitoring system using sulfur oxidizing bacteria (SOB) was tested to monitor WQ changes in real-time in natural stream water. The WQ monitoring system consisted of three SOB reactors (one continuous and two semi-continuous mode reactors). The SOB system did not detect any toxicity in relatively-unpolluted, natural stream water when operated for more than six months. When diluted swine wastewater (50:1) was added to the influent of the reactors, the system detected toxic conditions in both the continuous and semi-continuous operational modes, showing 90% inhibition of SOB activity within 1 h of operation. The addition of 30 mg/L NO 2 −-N or 2 mg/L of Cr6+ to the influents of SOB reactors resulted in the complete inhibition of the SOB activity within 1–2 h. The results demonstrated the successful application of an SOB bioassay as an online toxicity monitoring system for detecting pollutants from stream or river waters. Highlights • Biomonitoring of toxic chemicals is the most effective method in aquatic ecosystems. • Real time monitoring system based on sulfur oxidizing bacteria has been developed. • The SOB biosensor can detect toxic chemicals in continuous & semicontinuous modes. • The addition of 2 mg/L Cr6+ to SOB biosensor results in complete inhibition of SOB. [ABSTRACT FROM AUTHOR]