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Disentangling patterns of intra-specific changes in morpho-physiological traits is crucial for understanding the capacity of tree populations to cope with human-induced environmental changes. This study combined well established phenotyping techniques and unmanned aerial vehicle (UAV) imagery to characterise the extent of intra-specific variation for an array of meaningful traits among 18 populations of Pinus nigra growing in a common-garden experiment in central Spain, subject to summer drought. Data for eight traits describing aboveground growth, intrinsic water-use efficiency, water uptake patterns and reserve accumulation were obtained for 210 adult individuals belonging to the subspecies laricio, calabrica, nigra and salzmanii. UAV imagery was used to derive seven vegetation indices describing canopy structure and photosynthetic pigments. A strong inter-population differentiation arising from adaptation to cold and continental conditions at the geographical origin of the populations was found for growth traits, reserve accumulation, chlorophyll concentration and leaf surface area. Fast-growing populations, originating from milder climates, emerged in contrast to slow-growing populations, originating from colder and more continental areas of the species range. The latter were characterised by higher leaf chlorophyll concentration and higher investment in reserves. Inter-population variation was highly structured at the subspecies level. Subspecies laricio and calabrica were characterised by a higher growth investment, but diverged in relative radial to primary growth allometry, whereas subspecies nigra and salzmanii showed the highest investment in reserves. Importantly, variation of traits related to water economy was negligible, both at the population and subspecies level, indicating that Mediterranean populations of P. nigra may lack specific adaptation to drought stress. These results provided valuable information in forecasting the performance of this species in the context of climate change. Specifically, they anticipated the potential vulnerability of Mediterranean populations of P. nigra to future reduction in water availability.