As might be expected in an area close to a major river, in this case the Great Ouse, the local parishes contain a good deal of evidence of settlement before the Norman Conquest. The Bedfordshire Historic Environment Record [HER] details all these sites and find spots and is now on-line as part of the Heritage Gateway site. This article is taken from the various entries in the HER.

The earliest evidence for human activity in what is now Wyboston comes from a Neolithic handaxe in Bedford Museum [HER 14779]. Cropmarks east of the A1 at Wyboston Lakes [HER 1793] represent two probable ring ditches, one containing a rectangular feature. They were recorded on aerial photographs taken in 1959. Subsequent photographs taken in 1968 showed that the area had been quarried away. The ring ditches were probably the remains of late Neolithic or Bronze Age barrows.

Another ring ditch has been identified from a cropmark on smallholdings at Northfield Road [HER 16783]. More were identified from aerial photographs at Wyboston Lakes [HER 480]. They consisted of two possible rectangular enclosures, and four ring ditches. These were recorded as destroyed by gravel digging about 1958 or 1959.

Some cropmarks can only be tentatively described as prehistoric, without dating evidence from associated artefacts, no more precise dating is possible:

• HER 1882: cropmarks east of Rockery Road show a scatter of pits, and a probable palaeo-channel (i.e. an early watercourse, now dry), recorded from aerial photographs.
• HER 1881: cropmarks west of the Saint Neots bypass show a group of linear features in an aerial photograph; they do not form any obvious enclosures and are undated, but thought to be prehistoric.
• HER 13979: cropmarks south of Brook Farm form a linear series of separate sub-rectangular enclosures, extending for about 750 metres.
• HER 13980: cropmarks south of Eaton Tithe Farm form an extensive south-west to north-east orientated scatter of enclosures, in three groups: a rectilinear block; a curvilinear group and two polygonal marks which are conjoined.
• HER 16768: cropmarks south-west of Eaton Tithe Farm form an area of curvilinear enclosures. Nearby there are faint cropmarks of a rectilinear enclosure to the east, and a separate sub-rectangular enclosure to the north.

A group of rectangular enclosures observed on aerial photographs at Wyboston Lakes was examined before gravel extraction in the 1950s [HER 476]. The site proved to be a farmstead of the later Iron Age period, with later occupation in the Roman period, though it is unclear whether this was continuous or whether there was a break in occupation due to flooding of the site. The Iron Age occupation included two ring ditches indicating huts, and an inhumation burial part way down one of the enclosure ditches.

A site east of Little End, very close to the modern Cambridgeshire boundary has produced an enamelled decorative stud of 2nd century date, and a circular brooch of Iron Age or Roman date [HER 3239].