The Sustainable Development Goals have placed integrated resources management, such as integrated water resource management, at the heart of their targets. The upcoming “International Decade for Action—Water for Sustainable Development”, 2018–2028 has highlighted the importance of promoting efficient water usage at all levels, taking into account the water, food, energy, and environmental nexus. While integrated resource management approaches have been defined and applied for decades, nexus approaches are more recent. For these latter approaches to be implemented on the ground, their system boundaries need to be clarified. While the Water–Energy–Food Nexus focuses on sectors, the Water–Soil–Waste Nexus addresses linkages between environmental resources—namely water, soil and waste—to tackle sustainable management. In this paper, we analyzed integrated management systems and how their system boundaries are defined. From this we determined that in order for system boundaries to be applicable, they should be clear, wide and flexible. Based on this, we propose the boundary of the Water–Soil–Waste Nexus system. We use two case studies to exemplify the usefulness of these system boundaries.