We evaluated the ecophysiological responses of two semiarid coniferous tree species, Pinus halepensis and Tetraclinis articulata, growing on a nutrient-poor metalliferous mine tailings substrate to organic amendments (biochar and/or organic municipal waste). The trees were grown in mesocosms under irrigated conditions for 20 months. Then, a comprehensive characterization of soil and plant parameters (including stable isotopes) was carried out. Treatments containing municipal waste showed better soil fertility indicators (approximately 2-fold higher organic carbon and total nitrogen concentrations) and higher plant biomass (up to 5-fold higher) than unamended and only biochar treatments. Trees in most of the treatments exhibited leaf N/P ratios <14 indicating severe N limitation of plant growth. Metal uptake was below phytotoxic levels across all the treatments. Leaf δ13C values correlated positively with δ18O across treatments for both species indicating increasing water use efficiency with tighter stomatal regulation of water flux, and with T. articulata exhibiting tighter stomatal control (higher δ18O values) than P. halepensis. Trees in treatments containing only biochar did not differ in ecophysiological performance from those in the unamended treatments. In contrast, leaf stable isotopes revealed sharply increased of time-integrated photosynthetic activity (favoured by higher leaf N concentrations) combined with lower time-integrated stomatal conductance in the treatments containing municipal waste, indicating greatly enhanced water use efficiency in better nourished plants. Trade-offs between water use efficiency and nutrient (N and P) use efficiency were evident across treatments, with higher leaf nutrient concentrations associated with higher water use efficiency, at the cost of a lower nutrient use efficiency. These trade-offs were not impaired by the high metal concentrations of the tailings substrate, indicating that ecophysiological adjustments in response to changes in plant nutrient status promoted by the addition of organic amendments are critical for the adaptability of native tree species employed in the phytostabilisation of mine tailings. Display omitted •Organic amendments improve tree drought resistance and growth performance.•Better nourished plants were able to improve water use efficiency.•Metal uptake issues are not enough to fully explain tree adaptation to mine tailings.•A strong trade-off between water and nutrient use efficiency occurred in both trees.