Synthesis and quantification of disciplinary knowledge at the whole system level, via the process models of agricultural systems, are critical to achieving improved and dynamic management and production systems that address the environmental concerns and global issues of the 21st century. Soil physicists have made significant contributions in this area in the past, and are uniquely capable of making the muchneeded and exciting new contributions. Most of the exciting new research opportunities are trans-disciplinary, that is, lie on the interfacial boundaries of soil physics and other disciplines, especially in quantifying interactions among soil physical processes, plant and atmospheric processes, and agricultural management practices. Some important knowledge-gap and cutting-edge areas of such research are: (1) quantification and modeling the effects of various management practices (e.g., tillage, no-tillage, crop residues, and rooting patterns) on soil properties and soil-plant-atmosphere processes; (2) the dynamics of soil structure, especially soil cracks and biochannels, and their effects on surface runoff of water and mass, and preferential water and chemical transport to subsurface waters; (3) biophysics of changes in properties and processes at the soil-plant and plant-atmosphere interfaces; (4) modeling contributions of agricultural soils to climate change and effects of climate change on soil environment and agriculture; and (5) physical (cause-effect) quantification of spatial variability of soil properties and their outcomes, new methods of parameterizing a variable field for field-scale modeling, and new innovative methods of aggregating output results from plots to fields to larger scales. The current status of the various aspects of these research areas is reviewed briefly. The future challenges are identified that will require both experimental research and development of new concepts, theories, and models.