Calcareous fens are species-rich peatlands thought to form at discrete alkaline groundwater discharge points. Here the spatial and temporal variability in the peat pore-water hydrodynamics at a fine (plot) scale of three calcareous fens in southern Ontario was investigated over three growing seasons to evaluate the sensitivity of these wetlands to weather fluctuation and landscape position. Only a small area of the fens demonstrated patterns of groundwater upwelling, and positive vertical hydraulic gradients (VHG) were low, peaking at 0.1. Local decreases in saturated hydraulic conductivity generated areas of pore-water over-pressuring in the peat profile through much of the fens. Several areas were subjected to large negative VHG (max = −0.2), causing sustained groundwater recharge. In this study the strength of the connection to the principal source area of water (alkaline stream) determined the pattern and variability of calcareous fen peat hydrodynamics amongst three growing seasons differing markedly in precipitation. The range of pore-water hydrodynamics evident in this study provides evidence for the processes controlling the sensitivity of calcareous fens to climate and land-use change. A conceptual model linking calcareous fen landscape position to weather- and climate-induced hydrodynamic variability is presented to guide management of these biodiverse ecosystems.