Hydrochemical patterns across groundwater-fed wetlands, especially carbonate and redox gradients, can influence phosphorus (P) availability by controlling its distribution among different soil pools. We explored these linkages by comparing shallow (5–20 cm) soil properties along groundwater flowpaths in two rich fens, a marl fen, and a poor fen. Organic matter content, bulk density, and total elemental content varied more with depth to underlying drift materials than with water table fluctuation, but also were influenced by groundwater discharge, which stabilized water table elevations and controlled redox conditions. Total sulfur and calcium content increased where pore-water chemistry indicated active iron and sulfate reduction. Calcium mineral dynamics, however, did not appear to influence P availability: first, calcium carbonate (CaCO3) accounted for <2% of the soil composition, except in the marl fen where it accounted for 20–25% of the soil composition. Second, Ca-bound P pools, determined from hydrochloric extraction of wet soil samples, accounted for <25% of the inorganic soil P pool. In contrast, iron-bound P determined from bicarbonate-buffered dithionite solution, accounted for 50–80% of the inorganic soil P, and increased where there was evidence of groundwater mixing, as did P release rates inferred from incubated anion resin bags. The total carbon and phosphorus content of organic-rich soils as well as available and labile P pools were strongly correlated with pore-water iron and alkalinity concentrations. Groundwater discharge and resulting hydrochemical gradients explained significant variation in soil composition and P availability across each site. Results highlight the importance of conducting biogeochemical studies in the context of a site's shallow geologic setting and suggest mechanisms supporting the diverse plant species unique to groundwater wetlands.