Lake Cadagno displays a unique feature; two chemically very different water layers are permanently stratified over the seasons. A small transition zone separating the two layers presents steep physical and chemical gradients, really an unparalleled ecosystem.

The upper layer is in contact with the atmosphere and is similar to a common alpine lake which is fed by surface water from the snowmelt. In Lake Cadagno the main tributary originates from the Lago dello Stabbio flowing over granite rocks in the North; this water is low in minerals. 

The water in the lower layer of the lake lacks oxygen; it is fed by subaquatic springs from the dolomite. It is enriched in minerals and contains ions of the elements calcium, magnesium, sulfur, phosphorus and nitrogen. The high salinity causes a higher density of the water which stabilizes the lower part and slows down the mixing with the upper layer. This phenomenon is called meromixis, meaning only partial mixing during the seasons, mixing only in the upper part of the lake.

The zone where the two layers touch each other is called transition zone or chemocline. Here steep chemical gradients are found of oxygen (concentration decreasing with depth) and of reduced compounds (concentration increasing with depth)  such as hydrogen sulphide or ammonia.  Small amounts of light, about 1 to 5% of the surface sunlight, still reach this depth. Here at about 12 m the environmental conditions allow a massive growth of anaerobic phototrophic bacteria (e.g. Chromatium okenii), strongly increasing the primary production in the lake.