An 18-year field experiment was conducted on a highly acidic soil in the mixed farming zone of south-eastern Australia. The experiment was a fully phased design with three major treatment contrasts: perennial systems versus annual systems; unlimed versus limed treatments; and permanent pasture versus pasture-crop rotations. The hypotheses tested in this study were that a) perennial systems would be less acidifying than annual systems, and b) surface liming would lead to amelioration of subsurface soil acidity over time. Results showed that there was no significant difference in soil pH in terms of acidification rate and amelioration rate between perennial and annual systems, thus we rejected the first hypothesis. However, both perennial and annual systems did acidify or re-acidify soil. The re-acidification rate was at least 0.09 pH units per year in the 0–0.10 m depth under the limed treatment. The acidification rate was 0.005 pH units per year in the 0.10–0.20 m depth under the unlimed treatment. The vigorous lime regime of maintaining pH ≥5.5 (measured in 0.01 M CaCl2) in the 0–0.10 m depth increased soil pH in the 0.10–0.20 m depth at a rate of the 0.04 pH units per year, hence we accepted the second hypothesis. There was clear evidence of alkali movement vertically over time, but it was confined within the top 0.30 m depth over the 18-year period of experiment. It is recommended that soil should be limed regularly to maintain pH ≥5.5 to keep the system productive and sustainable.