Specialist ecosystems have developed on small areas (< 1 ha) of alkaline (pH 7–10) soil-free disturbed substrates in semiarid areas of southern New Zealand, where rare endemic plants are being outcompeted by adventive species as soil develops. We have conducted a pilot study for soil and weed removal at seven sites to increasing habitat availability for the rare plants. Six sites are on impermeable clay-altered schist where evaporation of marine aerosols in rain has formed localised NaCl-rich encrustations. These bare substrates host endemic salt-tolerant plants (halophytes), especially where electrical conductivity (EC) exceeds 1 mS/cm and excludes most weeds. One site is on limestone and associated erosional residues, where endemic calciflora have evolved on substrates that have pH of 7–8 and variable EC. Soil and weeds were removed to a depth of ~ 0.5 m, and the study plots were monitored for changes in substrate salinity, pH and plant colonisation for up to 1.5 years. The most successful saline plot, an abandoned mining area, had initial halophyte colonisation after 4 months, and after a year, the halophytes had achieved > 50% substrate coverage. The other saline plots also had lesser halophyte colonisation and more weed incursion. Bare limestone talus that had weeds allowed successful calciphyte germination. Parts of the limestone site where weeds and soil were removed had no calciphyte colonisation but significant weed development after 6 months. Our results suggest that soil removal is a viable management option for enhancing ecosystems that require bare substrates, preferably with deeper (~ 1 m) excavation.