Albert Einstein said that one should make everything as simple as possible, but not simpler. Likewise, biologists have often relied upon simplifying assumptions to study the fundamental properties of biological systems. To understand how complex multicellular plants respond to stresses such as high salinity, organ or organism-scale experiments have often been the standard and have led to important discoveries. However, recently, through the use of cell-type-specific analyses, it has become clear that most salt-stress regulation occurs at the scale of the cell or tissue type. Salt stress has been revealed to cause complex changes in growth, development and physiology that are dynamically regulated in both space and time. Thus, the next most important discoveries regarding how plants perceive, respond and adapt to this environmental stimulus will require approaches that enable high-resolution spatial and temporal observations to be made. In this review, we highlight studies taking both a genomic and sub-genomic approach to understand the salt response at high spatial resolution. These present and future studies will help lead to a more sophisticated understanding of the root as a complex system, which integrates information from different cell layers to generate synchronized changes necessary for the survival of the plant.