The consumption of water contaminated with bacteria poses significant health risks around the world, which brings into focus the need for the effective and efficient detection of microorganisms in water. Current technology for water-quality monitoring is based on frequent sampling and culturing methods which are time-consuming and do not allow a rapid decision making process. There is a clear need for rapid and more convenient analytical methods that enable their wide use and feed into regulatory and decision-making processes. PCR-based methods, DNA sequencing and immuno-fluorescence methods are promising strategies for pathogen detection. Development of new biosensing methodologies is currently under way that will open new avenues for the fast and cost-efficient detection of pathogens. In this review, we summarize recent advances and developments for monitoring pathogenic and biological agents in water samples.