With the fens impassable for much of the year Cottenham was effectively cut off on three sides by land. There was no road north to Twentypence until the nineteenth century, and no bridge there until the twentieth; the only reliable roads into the village were over the greensand ridge to the south. The parish must have felt much more isolated; it was not somewhere people had much reason to pass through, so it was not unreasonable to treat strangers with suspicion. The main route from Cambridge to the Isle of Ely didn't run along the line of the A10 to the east, but skirted the western edge of the Parish along Cuckoo Drift and Aldreth Causeway.
To compensate for the difficulties of land travel, water transport was common. All the fen edge villages had docks; Cottenham's were near the end of broad lane, with another landing place - 'the weights' - for deeper draft vessels near the church. The Roman Car Dyke was built for transport, not for drainage, and this was probably originally also true of Cottenham Lode, which may have been begun by the Romans. The original Lode ran from Broad Lane as far as the Car Dyke. In early medieval times it was possible to navigate from Cottenham north-west along the lode, then south-east on the Car Dyke, then north-west along a former continuation of the Clay Ditch watercourse to the Old West River, and thence to Cambridge, Ely or beyond. It was not until the seventeenth century that the present northern section of the Lode was added, linking straight to the Old West River; this made the Car Dyke largely redundant, and at some stage Clay Ditch was diverted into the straighter Beach Ditch. The section of Cottenham Lode running south-west from the village was not added until the nineteenth century.
After the severe inundations of the fourteenth century, a slightly drier climate and small improvements to local flood banks and ditches improved drainage, but the fens still flooded regularly. Most fenlanders were quite content with this; their livelihoods depended on the fish, fowl, reeds and sedge which flourished in the damp fens, and when more radical, large-scale drainage was proposed in the seventeenth century it met with widespread opposition. Cottenham was already better drained than many fenland parishes, and less dependent on the fen economy, but even here the winter flooding brought fertility to the land and further drainage was opposed.
Small-scale local projects, one of which led to the draining and enclosure of Adventurers' Fen in the early seventeenth century, could only make so much difference. The drainage of the Bedford levels in the late seventeenth century involved diverting much of the water that would have flowed into the Old West River along the newly dug Bedford Rivers. This must have had a significant effect on water levels in Cottenham, indeed on one occasion the villagers resorted to damming the river with barn doors in order to irrigate their fens.
Regional drainage schemes continued to improve during the eighteenth century, and wind pumps could be used to raise water from the lower lying land. None of these eliminated flooding in Cottenham, but they may have reduced it to the point where its beneficial effects were no longer so significant, so that by the early nineteenth century villagers were ready to embrace more substantial change.