Wagner Natural Area is underlaid by sand and gravel deposited at the end of the last ice age, approximately 10,000 years ago. These constitute an  
aquifer, allowing groundwater collected from catchment areas to the south of the Natural Area to flow down-slope through Wagner to the valley bottom in Big Lake, west of St. Albert. In low lying places where the ground dips below the water table, springs well up and the water flows overland. 

Much of this spring water is rich in calcium carbonate, typical of glacial gravel in the area. Other springs coming from deeper down contain sodium and sulfate. It is this abundance of mineral-rich water that creates Wagner's most distinctive type of plant community, the fens. Within the fens the water-filled hollows grade into larger marl ponds, so-called because in their shallow waters calcium carbonate precipitates from a supersaturated solution and is deposited as a whitish sludge or marl. 

Peat forms in waterlogged, low-oxygen conditions where plant remains cannot decompose fully. Core samples of peat taken from Wagner Natural Area indicated that peatlands have been present on the site for nearly 5,000 years. The conservation challenge is to preserve them in perpetuity, or at least to insulate them from human presence and activity. Considerable hydrogeological research has been undertaken in the Natural Area to determine the area of groundwater recharge (from precipitation), and direction and amount of groundwater in the flow channels. Wagner Natural Area is also recognised as one of Environment Canada's Ecological Monitoring and Assessment Network (EMAN) sites, and contains plant sample monitoring plots which are periodically assessed to determine exosystem changes over time. 

Aquifer: An underground layer of permeable rock, sediment (usually sand or gravel), or soil that yields water. The pore spaces in aquifers are filled with water and are interconnected, so that water flows through them.
Fen: A type of wetland fed by ground water and runoff, containing peat below the waterline.
Marl: a loose or crumbling earthy deposit (as of sand, silt, or clay) that contains a substantial amount of calcium carbonate.