The Downs surrounding Winchester are made of chalk laid down during the Cretaceous period some 75 -100 million years ago. The chalk is highly permeable and even heavy rains result in little surface run off, so the valley sides have no surface streams. Instead the chalk acts like a giant sponge and water drains through to natural aquifers, where the chalk is completely saturated. The water is released at a steady rate from springs when the chalk meets underlying non-porous rocks or where the Water Table reaches the surface.

Superficial deposits, clay, sands, gravels and silt overlie the chalk on the valley floor and in dry valleys on the valley sides. These are Quaternary deposits, eroded and laid down during the Ice Ages spanning the last 2.5 million years. The ground was frozen making the chalk impermeable but during interglacial's, and seasonally, large amounts of surface water carved out the pattern of branching valleys on the chalk slopes.

The spring fed River Itchen channel was cut during the later stages of the Ice Age, and partly filled with gravel, sands and silt, as water levels rose post glacially. This accounts for the multi braided meandering channels and the formation of low gravel terraces at the edges of the floodplain. The valley cuts through the chalk water table so there is a continuous base water flow into the river. The chalk streams on Clausentum Fen, although re-shaped by man, are part of this system.

The Fen, directly beneath the triple, branched dry valley of Stanmore, is situated below the edge of a gravel terrace, on the river alluvial deposits, but about a metre higher than the lower floodplain. Ground water flows within the chalk, and particularly in times of heavy rain, will be channelled down the slopes and may still seep into the Fen along the western edge.

The southern Fen, in places has deposits of silt more than 20 feet deep, where there was once a large mere.

The map is from the Geology of Britain Viewer (British Geological Survey materials - NERC 2017)