Technical Abstract: Quantitative system approaches, provided by process-based models of agricultural systems, are essential for optimizing the use of increasingly limited water and soil resources, guiding tactical management, and addressing the environmental concerns and global issues of the 21st century. Agricultural engineers have made significant contributions in the past to the development of such models and their applications in soil and water research, design, and management, and they are uniquely capable of making the much-needed and exciting further enhancements. Here, we present: (1) current status of system model development and applications in soil and water research and management, with examples of the USDA-ARS, Root Zone Water Quality Model (RZWQM); (2) lessons learnt from RZWQM development and applications that, based on our international collaborations and literature, shared with other models; and (3) future needs and directions in system model enhancements and applications to make them more effective. We make a strong case for international collaborations among modelers and experimentalists and for a common development/applications protocol and platform for the future.