Water relations of saplings of two Eucalyptus species (E. leptopoda Benth. and E. loxophleba Benth.) were investigated on engineered cover systems (soil spread over mine waste rock) with soil depths of 0.3, 0.5 and 0.7 m in a semi-arid climate during summer. Objectives were (1) to assess the influence of soil depth on plant water availability; and (2) to better understand the impact of water availability and diurnal environmental fluctuations on key physiological parameters such as transpiration (E), stomatal conductance (gs), net photosynthesis (A), intercellular CO2 concentration (Ci), and mid-day leaf water potential (ΨMD) as they relate to regulation of plant water status. Physiological responses of plants to environmental factors differed between plants in shallow versus deep soils and species. Plants on deeper soils were less affected by high vapour pressure deficit (VPD), temperature, and irradiance due to increased plant available water, partly provided by their less confined roots, resulting in higher overall gs, E, A, and ΨMD. Stomatal closure reduced A but not Ci, indicating that high temperature and radiation were also significantly contributing to the diurnal decline in A through reversible photoinhibition. Greater soil depth in natural (semi-) arid ecosystems and on constructed or restored substrates may minimise plant sensitivity to higher temperature, VPD and irradiance through plant available moisture, especially in areas most vulnerable to climate warming and drying.