We investigated seasonal variations in δ13C values and concentrations of carbohydrates and organic acids in needles of declining and healthy mountain pine (Pinus mugo ssp. uncinata (DC.) Domin) trees from the Swiss National Park (SNP), using compound-specific isotopes analysis (CSIA). Our goal was to study the impact of climatic drivers on the individual compounds and understand the reasons of partial tree declines in relation to healthy mountain pine trees under seasonal weather patterns. We found that temperature is the main climatic driver determining the seasonal carbon dynamics at the needle level. Lower seasonal δ13C variability and lower concentration levels of sucrose in needles suggest less photosynthetic activity and sink carbon demand in declining compared to healthy mountain pine trees. Higher concentration levels of hexose (glucose and fructose) can play a reserve function for surviving mechanisms of mountain pine trees. Seasonal patterns of organic acid (malate and citrate) suggest an increasing investment in maintenance and repair mechanisms. The seasonal course of carbohydrates and organic acids can therefore be considered an indicator for a modified carbon metabolism within the leaves and possibly within the other tree tissues, partially explaining the decline of mountain pine trees.