Managing water resources to meet current social, economic, and environmental needs without compromising the ability to meet those needs in the future, requires water managers to look beyond jurisdictional boundaries and their immediate supply operations, protect shared water and marine environments, resources and ecosystems from pollution and over-abstraction and deliver structural changes and resilient solutions to make the provision of water services sustainable. With a plethora of system tools increasingly available to support the sustainability transformation of water systems, sorting through their breadth and diversity to determine what is useful and what is not can be challenging. From a selection of 40 popular system tools grouped in terms of how they function, we review those most commonly used in water management through 35 water-related studies from the literature. Findings demonstrate that system tools are not a substitute for systems thinking and applying them alone does not qualify the development of systemic solutions. Systems thinking offers a powerful approach to first improving collective understanding of sustainability challenges related to water and then, in collaboration with a diverse group of stakeholders and the public, defining desired goals for water management and working together to make them a reality. System tools in that context can play an important role in facilitating the process and here we propose an overarching framework of how to select and apply available tools to facilitate a holistic, integrated, and interdisciplinary systems approach for water management and wider urban sustainability transitions.