Bonby is one of the 'low villages'; spring-line communities, at the foot of the North Lincolnshire Wolds, on the eastern edge of the Ancholme valley.

First recorded as 'Bundebi' in 1086 the spelling of the village name has altered over the years, appearing as Bundebi, Bondebi and Bondby. It is not entirely clear whether the village derives its name from a particular family connection or by more general reference to the 'peasant's farmstead or hamlet'

The Parish is three and three quarter miles long by one mile wide, stretching from the banks of the Old River Ancholme in the southwest to the A15 Principal Road in the northeast. Approximately half of the area of the Parish is high Wold, intensively farmed but with a thin, chalky soil. Much of the remainder of the Parish is reclaimed river floodplain. This valley-bottom land, or 'carr', was once the bed of a glacial lake; the soil, a rich sandy-loam, supports a wide range of crops.

The village occupies the narrow band of rising ground between the carr land and the steep escarpment of higher Wold. This part of the Parish is a mixture of glacial sands and gravel and post-glacial wind-blown sands. Many of the early buildings in the village were built using Chalk, a weak rock but durable when dry. Few of these old Chalk buildings survive, with the notable exception of the early thirteenth century Parish Church, but there are isolated examples of Chalk walling dotted round the village.

The springs, that formerly supplied the village with its water supply, still flow from wooded combes on the edge of the Wold. The streams fed by these springs are all piped through the village but issue again into drainage dykes that carry the water across the low-lying 'Carr', to out-fall into the wide channels that drain these levels.