Water quality prediction, a well-established field with broad implications across various sectors, is thoroughly examined in this comprehensive review. Through an exhaustive analysis of over 170 studies conducted in the last five years, we focus on the application of machine learning for predicting water quality. The review begins by presenting the latest methodologies for acquiring water quality data. Categorizing machine learning-based predictions for water quality into two primary segments—indicator prediction and water quality index prediction—further distinguishes between single-indicator and multi-indicator predictions. A meticulous examination of each method’s technical details follows. This article explores current cutting-edge research trends in machine learning algorithms, providing a technical perspective on their application in water quality prediction. It investigates the utilization of algorithms in predicting water quality and concludes by highlighting significant challenges and future research directions. Emphasis is placed on key areas such as hydrodynamic water quality coupling, effective data processing and acquisition, and mitigating model uncertainty. The paper provides a detailed perspective on the present state of application and the principal characteristics of emerging technologies in water quality prediction.