Agent-based modeling (ABM) has been widely applied in water science, covering a wide range of research topics, from evaluating the efficiency of water management strategies at the macroscale to simulating microbial and algal colony reactions at the microscale. The capability of ABM for simulating how system performance is affected by individuals' behaviors and reactions makes it an ideal tool for representing complex adaptive systems in the real world. This paper provides a comprehensive review of the application of ABM in water science and identifies the current common problems. Several potential solutions to the problems were discussed, including (1) employing standard methods for validation, (2) adopting the ODD (Overview, Design, and Details) protocol and ODD+D (ODD + Decision) protocol to enhance readability and reproducibility of the model, and (3) applying a scaling-down approach and superindividual approach to reduce model complexity and facilitate computational efficiency.