The first analysis of chloride fluxes and compartmentation in a non-excised plant system is presented, examining ten ecologically pertinent conditions. The short-lived radiotracer couple 38Cl/39Cl was used as a Cl− tracer in intact barley (Hordeum vulgare L. cv. Klondike) seedlings, which were cultured and investigated under four external [Cl−], from abundant (0.1 mM) to potentially toxic (100 mM). Chloride–nitrogen interactions were investigated by varying N source (NO3− or NH4+) and strength (0.1 or 10 mM), in order to examine, at the subcellular compartmentation level, the antagonism, previously documented at the influx level, between Cl− and NO3−, and the potential role of Cl− as a counterion for NH4+ under conditions in which cytosolic [NH4+] is excessive. Cytosolic [Cl−] increased with external [Cl−] from 6 mM to 360 mM. Cl− influx, fluxes to vacuole and shoot, and, in particular, efflux to the external medium, also increased along this gradient. Efflux reached 90% of influx at the highest external [Cl−]. Half-times of cytosolic Cl− exchange decreased between high-affinity and low-affinity influx conditions. The relationship between cytosolic [Cl−] and shoot flux indicated the presence of a saturable low-affinity transport system (‘SLATS’) responsible for xylem loading of Cl−. N source strongly influenced Cl− flux to the vacuole, and moderately influenced Cl− influx and shoot flux, whereas efflux and half-time were insensitive to N source. Cytosolic pool sizes were not strongly or consistently influenced by N source, indicating the low potential for Cl− to act as a counterion to hyperaccumulating NH4+. We discuss our results in relation to salinity responses in cereals.