Non-invasive microelectrode ion flux measuring (the MIFE system) allows concurrent quantification of net fluxes of several ions with high spatial (several μm) and temporal (ca 5 s) resolution. Over the last 10 years, the MIFE system has been widely used to study various aspects of salt stress signaling and adaptation in plants. This chapter summarizes some major findings in the area such as using MIFE for deciphering the specific and non-specific components of salinity stress, resolving the role of the plasma membrane H+ -pump in salinity responses, proving K+ homeostasis as a key feature of salinity tolerance, and discovering the mechanisms behind the ameliorative effects of Ca2+ and other mitigating factors (such as polyamines or compatible solutes). The full protocols for microelectrode fabrication, calibration, and use are then given, and two basic routines for measuring net K+ and Na+ fluxes from salinity stressed roots are described in the context of plant screening for salt stress tolerance.