Microbial contamination of water resources causes a huge socio-economic impact as illustrated by the frequent outbreaks in developed and resource constrained countries. To combat potential threat an efficient detection/monitoring system as well as decontamination system is required. A plausible approach balancing these important aspects will check the dissemination of virulent and multi-antimicrobial bacterial pathogens in the environment. Despite the recent advances in the detection and decontamination of bacterial pathogens from water, there still exist many challenges and opportunities to improve the applicability of these methods on a large scale or in samples from complex environments. The rapid detection techniques include quantitative polymerase chain reaction (qPCRs), oligonucleotide DNA microarrays and next generation sequencing (NGS) that have paved way for rapid and sensitive detection of bacterial pathogens. The advancement in nano-biotechnology has empowered miniaturization of devices and accelerated the development of advanced on-site/on-time microbial detection tools and new decontamination technologies. The principle, sensitivity, application and challenges of the molecular methods for the detection and characterization of bacterial pathogens have been presented in this review. The second part of review addresses the decontamination methods specifically highlighting the applicability of photocatalytic nanoparticles. An overview of current efforts and technical innovations in detection and decontamination strategies for aquatic microbial load specifically bacteria have been presented. The review highlights the need towards development of a system capable of detection as well as elimination of bacteria from environment to reduce human health risk.