The aim of this study was to quantify the effect of different varieties, planting densities, tree training systems and canopy aspect (north and south) on tree water use efficiency and nitrogen (N) availability in relation to mango fruit yield and fruit size as well as soil fertility (particularly total carbon (C) and total N as well as C and N isotope compositions) in a 5-year-old mango plantation of tropical Australia. Material and Methods Mango foliar samples were collected from a 5-year-old, factorial field experiment, where we tested the effects of two mango varieties (Calypso vs Keitt); two planting densities (medium vs high); two training systems (single leader vs conventional); and two sampling canopy aspects (north vs south) on foliar total C (%), total N (%), and stable C and N isotope compositions (δ 13 C and δ 15 N). The 0-10 cm of surface soils were also assessed for total C, total N, and δ 13 C and δ 15 N of different varieties, planting densities, and training systems. In addition, mango fruit yield, and fruit size were measured. Results There were significant genetic effects on foliar total N, tree water use efficiency (WUE) as reflected by foliar δ 13 C, N availability as indicated by foliar total N and δ 15 N, mango fruit yield, and fruit size in 5-year-old mango trees in tropical Australia. Overall, Keitt had higher foliar δ 13 C and N availability (higher total N and lower δ 15 N) as well as higher mango yield and greater fruit size, compared with those of Calypso. There were also significant environmental influences on foliar δ 13 C and N availability. In particular, high planting density had higher N availability (higher total N), and lower foliar δ 13 C as well as higher N loss (higher δ 15 N), compared with those of medium planting density. High planting density treatment also had higher soil total N, compared with that of medium planting density treatment. The conventional training system had higher N availability and foliar δ 13 C, compared with those of the single leader training system. The northern side of tree canopy (sunny side) had lower fruit number, compared with that of the southern side (shady side) of tree canopy. Conclusion There were significant genetic and environmental influences on tree WUE and N availability as well as mango fruit yield and fruit size in the 5-year-old mango trees. Among them, Keitt's fruit was significantly larger than Calypso and had higher foliar δ 13 C (higher WUE). Although high planting density increased soil total N, it also resulted in lower foliar δ 13 C and more N loss. Our results highlighted the significant potential for improvement of foliar δ 13 C and N availability as well as fruit yield and soil fertility with both genetic selection and site management regimes.