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Although the station is responsible for pumping the area of the Black Sluice Internal Drainage Board, it is operated by the Environment Agency, not the Board. This resulted from the Sluice and the South Forty Foot Drain being taken over by the Witham and Steeping Rivers Catchment Board in 1935, then passing to the Rivers Authority and finally to the Environment Agency..

The northern part of the Station was the original pumping station, opened in 1946 with 3 Ruston 900hp pumps. Requirements for additional pumping in its area by the IDB resulted in a need for additional pumping capacity at Black Sluice. The then operator, the Lincolnshire Rivers Board, added two further pumps, by English Electric of 975 hp, in a southern extension to the building. An information panel outside the station states that there have only been three occasions, in 1968, 1977 and 1981 when all five pumps have been run together.

There was a lock at the sluice until 1971, although there is no evidence for a right of navigation on the drains. However, following pressure to revitalise leisure navigation on the drains, a new lock was opened in 2009 as part of the Fens Waterway Link.

A history of the IDB can be found here Link