It contains 130 hectares (320 acres) of land and predominantly comprises calcareous fens alongside marl ponds, wetland meadows, and forests of black spruce and tamarack.

However one issue unresolved by the protective designation is that most of the groundwater reservoirs that feed the fens are outside of the Wagner Natural Area itself.

Although forty acres of wetlands were cleared and filled by the Wagner family, the plan was ultimately unsuccessful, possibly due to sinkholes or the presence of seaside arrow-grass, which can be toxic to cattle and taint their milk.

[5] Wagner sued the CPR due to their plans to dynamite the area in order to mine the marl to make cement.

Peatlands, such as Wagner, are uncommon within this sub-region, as it approaches the southern geographical limit of distribution due to microclimate and edaphic influences.

Wagner Natural Area sits within the wettest part of the sub-region, due to available moisture increasing along a gradient from the southeast to northwest.

As a result of Pleistocene glaciation, sand and gravel deposits form the major aquifer in Wagner Natural Area.

The spring water remains at a temperature around 4 °C (39 °F) year round, preventing the deep frost from freezing the area during harsh Alberta winters.

There is a 1.5 kilometre trail that loops around the marl ponds and includes benches, outhouses, a picnic shelter, and a boardwalk to prevent damage to the fen itself.

[11] In 1988, Alberta Transportation announced its intention to build a road connecting the Yellowhead Highway to a new bypass in Edmonton.

[10] In 2007, the Parkland County considered a draft proposal to rezone the lands along its southern boundary, including Wagner Natural Area, from agricultural to industrial.

The construction of roads, sewers, and water lines would have a severe negative impact on Wagner as a wetland because, as a fen as opposed to a bog, it is dependent on groundwater sources, most of which are outside of the protected borders of the area.