‘Space-for-time’ approaches can help assess the capacity of species to locally adapt and acclimatise to heterogeneous environmental conditions. Fjords make ideal models for such studies, as they form environmental mosaics and isolate populations. Integrating genomics, metabolomics and environmental profiling, we investigated whether copepods (Calanus glacialis) inhabiting fjords spanning a broad Arctic-subarctic latitudinal gradient differ in their response to ocean acidification. Single-nucleotide polymorphism data reveal a clear population genetic structure among copepods from the four studied fjords, positively associated with latitude and seawater temperature. Fjords exhibit contrasting physico-chemical environments, with a wide range of pH, where the southernmost (Lurefjorden, Southern Norway) and northernmost (Billefjorden, Svalbard) fjords present the lowest pH minima. Targeted metabolomics reveals that inter-population variation exists in copepods’ response to acute experimental ocean acidification. In particular, range-edge populations show the greatest metabolomic sensitivity to ocean acidification, correlating with the higher dissolved inorganic carbon content they experience in their fjords. However, the northernmost and southernmost populations utilise different metabolic strategies. At the southern edge, copepods are smaller with higher metabolite levels, and rely predominantly on the citrate cycle. Conversely, copepods from the northern locality are larger and have lower metabolite levels, forcing them to rapidly switch to amino acid catabolism and anaerobiosis. Overall, coupling genomics, environmental profiling and metabolomics phenotyping, we demonstrate that habitat heterogeneity along the Arctic-subarctic gradient makes range-edge populations more sensitive to ocean acidification, consistent with their local adaptation to low seawater pH. Our work pinpoints range-edge populations as priorities for conservation efforts in the future ocean.