Widespread demand for the analysis and control of water quality and supply for human activity and ecosystem sustainability has necessitated the continuous improvement of water analysis methods in terms of their reliability, efficiency, and costs. To satisfy these requirements, flow-injection analysis using different detection methods has successfully been developed in recent decades. This review, based on about 100 original research papers, presents the achievements in this field over the past ten years. Various methodologies for establishing flow-injection measurements are reviewed, together with microfluidics and portable systems. The developed applications mostly concern not only the determination of inorganic analytes but also the speciation analysis of different elements, and the determination of several total indices of water quality. Examples of the determination of organic residues (e.g., pesticides, phenolic compounds, and surfactants) in natural surface waters, seawater, groundwater, and drinking water have also been identified. Usually, changes in the format of manual procedures for flow-injection determination results in the improvement of various operational parameters, such as the limits of detection, the sampling rate, or selectivity in different matrices.