The ground flora would have been typical wet fen species and species of open water pretty much as is found at Chippenham and Wicken fens. Comprising many species of sedges, rush, reeds, bulrushes, bog bean, loosestrife and gypsywort. As the ground became drier then more ornamental species could move in such as loosestrife, greater burnet, marsh pea, marsh woundwort, orchids, devils bit scabious, marsh marigold etc. As the trees took over then faster moving hedge species could colonise such as lord and ladies, hedge mustard, cow parsley, primroses, geum. The ancient wood flora would be so slow moving that it would be unlikely to have spread much from the peninsula but would consist of plants such as bluebells, oxslips, anemones and paris.
On higher ground such as Mitchell Hill and Bullocks Haste and most of the peninsula there would have been oaks, willows, ash, apple, hawthorn, buckthorn, blackthorn and elm. Privet, guelder rose, wild rose, brambles would also have been common. Hedge and ancient wood flora would have predominated beneath these. Fenland in the parish has all been lost through drainage, straightening of watercourses and peat digging for fuel - this, combined with ploughing, has almost completely removed evidence of peat in the soil.
Some relict wet fen flora survives in ditches, ponds and gravel pits. Dryer fen flora, such as can still be found at Wicken and Chippenham, has all disappeared. This disappearance was entirely due to the enclosures and was resisted by the villagers who valued the rich meadows they were losing for the annual hay crop. Meadows of the type that would have been common round Cottenham still survive at Soham.