The presence of microorganisms in waters is of great public concern and the trouble of detecting them in water is even well known. The traditional culture methods used for detection of environmental and pathogenic microorganisms are often not very sensitive and tend to underestimate the actual microbial load. Furthermore, the laboratory techniques used for their isolation and quantification commonly give results within some days after sampling. Thus, all the commonest methods for the microbiological examination of water are retrospective. In most cases, the time needed for results can represent a substantial problem, since possible microbial contamination can be confirmed when public health has been already jeopardized. Consequently, the use of procedures that provide rapid results becomes of fundamental importance. A variety of analytical approaches have been proposed for the rapid detection of microorganisms in water and the development of new and improved methods for microbiological water analysis is a continuous process. Advances in molecular biology for 20 years have increased the knowledge of microorganisms in water and molecular biology-based methods, notably those utilizing qualitative and quantitative PCR technology, have shown particular promise. These non-cultural methods are of great interest because their high throughput allows the detection of not cultivable bacterial indicators and pathogens and are less time-consuming. For a rapid bacterial detection, biosensors have also been developed in recent years. Even techniques such as flow cytometry and immuno-magnetic separation are rapid, quantitative and versatile methods because can be combined with nucleic acid probes and immune fluorescence to monitor viability. The advent of next generation sequencing (NGS) platforms has revolutionized DNA sequencing by allowing massively parallel sequencing with millions of reactions running in the same experiment. New platforms (e.g., Illumina, Ion Torrent) have been introduced during the last decade, and NGS has rapidly become an invaluable tool for the detection, identification and relative quantification of environmental microorganisms. The growing accessibility of NGS methods will greatly increase our understanding of microbial diversity in water environments. In this review, some of the most innovative and promising analytical techniques are described. •Microorganisms in waters are of great public concern and the trouble of detecting them in water is even well known.•Traditional culture methods are retrospective and tend to underestimate the actual microbial load.•Consequently, the use of procedures that provide rapid results are of fundamental importance.•A variety of analytical approaches has been proposed for the rapid detection of microorganisms in water.•The development of new and improved methods for microbiological water analysis is a continuing process.•Some of the most interesting and promising analytical techniques for water microbiological analysis are described.