The first people to modify the fen drainage were the Romans who developed rivers as transport routes and began drainage.

During the Dark Ages, food was produced, in the form of wildfowl, fish and, of great importance, eels. Sedge and reed were cut for thatching, turf for fuel, and litter (hay) for fodder and bedding. This lifestyle persisted in some places right up into the 19th century.

There were several attempts at drainage in the 13th and 14th centuries. By the middle of the 17th century, technology had advanced to permit more permanent, large-scale solutions. One of these projects was undertaken by Sir Cornelius Vermuyden, a Dutch engineer. The investors who paid for the work were known as 'Adventurers'. They were to be repaid in land once drainage was complete.

Drainage was not welcomed by all, and many inhabitants of the fens feared for their livelihood and traditional way of life. These fears led to riots in such places as Soham and Wicken.

An unforeseen problem arose when Vermuyden's works began - the peat shrank when drained. As the peat dried, air and bacteria broke down the previously undecayed plant remains and the surface level dropped. Soon the level of the peat in the drained areas fell to that of the rivers and the fens once again became flooded. Only by embanking rivers and pumping water up from the shrinking farmland could the fens continue to be used for agriculture.

In some areas today the peat has shrunk so much that the bog-oaks are being uncovered together with underlying clay.

The drainage of the fens and the use of land for agriculture altered the way of life of the people and drastically affected the wildlife. Most species of plant and animal of natural fenland suffered decline and some became extinct.

Wicken Fen escaped the fate of the rest of the fens largely because of sedge. This regular crop, dating back to at least 1414, bought trade to the area. Draining Wicken Fen would have destroyed the lucrative sedge harvest. The land around Wicken Fen was extensively drained and started to shrink.

When peat digging and crop harvesting declined in the late 19th century it was eventually suggested that the area, like nearly every other, should be drained for agriculture. Wicken had by then been discovered by naturalists, particularly entomologists, for whom it had become a valuable collecting site.