The selection of drought-tolerant genotypes is globally recognized as an effective strategy to maintain the growth and survival of commercial tree species exposed to future drought periods. New genomic selection tools that reduce the time of progeny trials are required to substitute traditional tree breeding programs. We investigated the genetic variation of water stress tolerance in New Zealand-grown Pinus radiata D. Don using 622 commercially-used genotypes from 63 families. We used quantitative pedigree-based (Genomic Best Linear Unbiased Prediction or ABLUP) and genomic-based (Genomic Best Linear Unbiased Prediction or GBLUP) approaches to examine the heritability estimates associated with water stress tolerance in P. radiata . Tree seedling growth traits, foliar carbon isotope composition (δ 13 C), and dark-adapted chlorophyll fluorescence (Y) were monitored before, during and after 10 months of water stress. Height growth showed a constant and moderate heritability level, while the heritability estimate for diameter growth and δ 13 C decreased with water stress. In contrast, chlorophyll fluorescence exhibited low heritability after 5 and 10 months of water stress. The GBLUP approach provided less breeding value accuracy than ABLUP, however, the relative selection efficiency of GBLUP was greater compared with ABLUP selection techniques. Although there was no significant relationship directly between δ 13 C and Y, the genetic correlations were significant and stronger for GBLUP. The positive genetic correlations between δ 13 C and tree biomass traits under water stress indicated that intraspecific variation in δ 13 C was likely driven by differences in the genotype’s photosynthetic capacity. The results show that foliar δ 13 C can predict P. radiata genotype tolerance to water stress using ABLUP and GBLUP approaches and that such approaches can provide a faster screening and selection of drought-tolerant genotypes for forestry breeding programs.