Abstract Aapa mires are boreal peatland complexes comprised of wet, typically patterned fens in the center and Sphagnum bog vegetation at the margins. Their distribution is controlled by climate and local catchment hydrology. The daily discharge of twelve aapa mires across the boreal zone was explored for 1961–2099, with the CPIsnow model using observational weather data and projections based on climate models (CMIP5) and emission scenarios (RCP4.5 and RCP8.5). Mire hydrology was assessed for climate-zonal differences, seasonal patterns, and longer-term trends. The results indicated past and future changes in hydrology, particularly related to the duration and magnitude of snow cover and the timing of snowmelt. Increasing winter discharge and decreasing spring discharge were detected in recent past in the southern sites, and these trends were indicated to continue in the future throughout the study area. By the end of the 21st century, the typical seasonality of discharge is indicated to weaken throughout the study area and to largely disappear in the south boreal catchments. In the northernmost sites, a mismatch between past trends and future projections of spring discharge was discovered, indicating complexity and uncertainty of snow process modeling. The hydrological changes indicated in this study, together with direct impacts of increasing temperatures, threaten aapa mires, affecting biodiversity and greenhouse gas balance. In changing climate, special attention should be paid to winter conditions and snow, essential for the hydrological cycle in the north but under-explored in mire hydrology studies.