The main goal of this review is to summarize practical approaches concerning the application of microfluidic systems for the analysis of various biomarkers and pollutants, as well as microbes, in water and wastewater matrixes. This problem involves multidisciplinary expertise combining research knowledge from various areas, including wet chemistry, biochemistry, physical chemistry, molecular biology, genetics, signal processing, microelectronics material science, and separation science. It has been documented that fairly primitive but fast and inexpensive screening methods involving paper-based analytical devices (PADs) and micro total analytical systems (μTAS) can be considered as serious alternatives to their more advanced counterparts such as GC, HPLC, and capillary electrophoresis coupled to various sophisticated detectors (e.g., multiwavelength spectrophotometers such as UV-Vis/DAD and mass spectrometers). The main advantage of PAD- and μTAS-driven technology is that such sensing devices may work under on-site and real-time conditions and measure a number of physical parameters and chemical factors simultaneously. Moreover, hybrid miniaturized analytical systems may combine sensing and data acquisition modules with common mobile phones and electronic devices working with global positioning systems and communicating through the Internet.