Peat specific yield (SY) is an important parameter involved in many peatland hydrological functions such as flood attenuation, baseflow contribution to rivers, and maintaining groundwater levels in surficial aquifers. However, general knowledge on peatland water storage capacity is still very limited, due in part to the technical difficulties related to in situ measurements. The objectives of this study were to quantify vertical SY variations of water tables in peatlands using the water table fluctuation (WTF) method and to better understand the factors controlling peatland water storage capacity. The method was tested in five ombrotrophic peatlands located in the St. Lawrence Lowlands (southern Québec, Canada). In each peatland, water table wells were installed at three locations (up-gradient, mid-gradient, and down-gradient). Near each well, a 1-m long peat core (8 cm × 8 cm) was sampled, and subsamples were used to determine SY with standard gravitational drainage method. A larger peat sample (25 cm × 60 cm × 40 cm) was also collected in one peatland to estimate SY using a laboratory drainage method. In all sites, the mean water table depth ranged from 9 to 49 cm below the peat surface, with annual fluctuations varying between 15 and 29 cm for all locations. The WTF method produced similar results to the gravitational drainage experiments, with values ranging between 0.13 and 0.99 for the WTF method and between 0.01 and 0.95 for the gravitational drainage experiments. SY was found to rapidly decrease with depth within 20 cm, independently of the within-site location and the mean annual water table depth. Dominant factors explaining SY variations were identified using analysis of variance. The most important factor was peatland site, followed by peat depth and seasonality. Variations in storage capacity considering site and seasonality followed regional effective growing degree days and evapotranspiration patterns. This work provides new data on spatial variations of peatland water storage capacity using an easily implemented method that requires only water table measurements and precipitation data.