ABSTRACT The Patearoa saline site in Maniototo basin has developed on variably clay-altered Otago Schist. Decomposition and sedimentary redistribution of schist outcrop components has led to formation of bare soil-free substrates (upper metre scale) with contrasting permeability to rain and shallow groundwater percolation. Relatively impermeable clay-rich substrates, with a surface crust (cm scale) of detrital clay and muscovite, are saline with electrical conductivity (EC) of 1–35 mS/cm and locally hyperalkaline (pH > 10), with evaporative mineral accumulations. These saline substrates are downslope of more permeable substrates consisting of coarse schist debris and fractured outcrops, which have lower salinity (EC < 1 mS/cm) and lower pH (<7). A salt line can be mapped at metre scale between these substrate types on hillsides. The geochemical contrasts across the salt line have strong effects on plant communities that are colonising bare ground. Initial colonisation of bare saline substrates by some plants changes the geochemical signatures of the surficial few centimetres to form proto-soil with lower EC and pH. Proto-soil development facilitates further colonisation by pasture grasses, but the underlying substrates remain saline and highly alkaline. Salt lines similar to the one at Patearoa are mappable elsewhere in the Otago area and constitute fundamental geoecological boundaries.