Three main ecosystems make up the Grande Cariçaie:

 the lakeside shallows: continuously covered by a few centimeters to a few meters of water, they foster Potamogeton and Characea algae communities

 the unwooded meadows: continuously saturated by the water table and sometimes flooded by the lake, they consist mainly of reed and tall-sedge plant communities

 the riparian forests: often saturated by the water table, they consist of mixed forests, pine forests (a very particular plant community in Switzerland), willow forests, alder forests and poplar plantations.

Behind these moist ecosystems, a hillside forest separates the wetlands from the agricultural landscape. This sandstone hill marks the former location of the lake’s shore, before the process known as the "première correction des eaux du Jura" (first Jura lakes correction) took place at the end of the 19th century.