The occurrence of the viable but nonculturable (VBNC) state in bacteria indicators (i.e. Enterococci) constitutes a significant health problem as these bacteria may escape from current culture-based detection. This study aims to develop a sensitive and rapid method to detect all viable enterococcal cells including those in the VBNC state in tropical surface waters, and to understand their significance in surface waters. Propidium monoazide (PMA) pre-treatment was optimized to reduce the impact of false positive signal from dead cell in quantitative PCR (qPCR). A new primer and probe set which targets the penicillin binding protein 5 (pbp5) gene, was designed to achieve very sensitive and specific detection of viable E.faecalis. This study systematically investigated the decay kinetics of E.faecalis under different environmental stresses using both culture-based method and PMA-qPCR method. Mathematical models were developed to predict the occurrence of the VBNC cells under stressed conditions.