Patterned bog and fen peatlands, which dominate the landscape in the Hudson Bay Lowlands (HBL), act as important water storage and conveyance features in this region. In spite of their hydrological importance, there are currently no studies that define and characterize the thresholds of bog‐fen‐tributary hydrological connectivity in the HBL or their relation to seasonal and annual changes in water fluxes. To this end, hydrological (i.e., streamflow and groundwater levels) and meteorological (i.e., precipitation, snow depth, evapotranspiration, and temperature) data were collected at a 4.8 km2bog‐fen‐tributary complex between 2007 and 2018. Connectivity thresholds were best characterized into three states (disconnected, connected, and high activity) that incorporated 41%, 47%, and 12% of the study period and 4%, 18%, and 78% of runoff, respectively. Runoff generally peaked in the spring due to snowmelt, while connectivity was highest in the peatlands in the fall months when precipitation exceeded evapotranspiration due to cooling temperatures. Warmer than average spring temperatures accelerated snowmelt rate faster than frost table thaw rate in the fen; this reduced the amount of meltwater that entered storage, increased drainage from bog to fen, and decreased overall connectivity in the unfrozen season. Cooler than average spring temperatures delayed bog connection and ground thaw; the late frost melt provided a source of water to the bogs after melt into the late spring and early summer. This study provides a basis for the modelling of peatland hydrological connectivity in the region in the drier conditions anticipated with climatic warming and regional resource extraction.