Scots pine (Pinus sylvestris L.) is adapted to various soil types with diverse water availabilities. However, Scots pine seedlings are vulnerable to abiotic stress during the early growth, when they may be exposed to both dry and wet conditions. Here, we focused on the above and below ground coping strategies of Scots pine seedlings under controlled wet, optimal and dry soil conditions by investigating morphological traits including seedling biomass, number of root tips, proportion of mycorrhizal root tips and brown needles. In addition, we studied metabolic and physiological responses including gene expression involved in biosynthesis and catabolism of polyamines (PA), PSII efficiency and the expression of the catalase (CAT) late-embryogenesis abundant protein (LEA), pyruvate decarboxylase (PDC), glutamate-cysteine ligase (GCL) and glutathione synthetase (GS) genes. We found that seedlings invested in shoots by maintaining stable shoot water content and high PSII efficiency under drought stress. Free and soluble conjugated putrescine (Put) accumulated in needles under drought stress, suggesting the role of Put in protection of photosynthesizing tissues. However, the expression of the PA biosynthesis genes, arginine decarboxylase (ADC), spermidine synthase (SPDS) and thermospermine synthase (ACL5) was not affected under drought stress whereas catabolizing genes diamino oxidase (DAO) and polyamine oxidase (PAO) were down-regulated in shoots. The morphology of the roots was affected by peat water content. Furthermore, both drought stress and water excess restricted the seedling ability to sustain a symbiotic relationship. The consistent pattern of endogenous PAs seems to be advantageous to the Scots pine seedlings also under stress conditions.