When exactly the ponds were created in the former bog and heathland, so far could not be determined. A congestion concession dates from 1842; but the waters are likely to have existed long before. As the Prussian first recording of 1837 shows, there was originally a third pond in the area of the nature reserve. It was below the western pond and about the same size. The today's alder break was therefore much smaller. The western limit of this pond was located approximately where today the high voltage power line runs.
The scientific significance of the Kipshagen ponds has long been known. Therefore, there was an early effort to preserve the area for posterity. In 1925 it was secured by a lease between the former owner, the landowner Kipshagen and the Natural Science Association Bielefeld. However, a purchase of the area by the club did not materialize. As early as 1932, the area had to undergo numerous interventions. For example, a larger moorland complex on the upper pond was covered with sand, and the pond floor was fertilized with lime and cleared away. A floristic particularly valuable moorland sink in the southwest of today's NSG was completely destroyed.
In 1937, the area was finally placed under conservation for the first time. This makes it one of the oldest protected areas in the Senne, alongside the Langenberg Pond, the Ramselbruch and the Furlbachtal. Despite the early underprotection, the condition worsened rapidly in the following years. In 1942 the Epping company was authorized to store waste near the nature reserve and to trickle sewage. After the war, recreational activities in the area increased significantly; in the ponds was bathed. On the Paderborn weekly market also water lilies and lung enzymes were sold, which had been taken from the area. Although a new protection order was issued in 1970; however, the protected area was reduced to 7.8 ha. The most serious consequences for the vegetation had the discharge of wastewater, which eventually led to a loss of the once very rich riparian and floating leaf vegetation (water lilies).
At the end of 1989, extensive care and restoration work was carried out in the area. In order to protect the transitional moor against increasing eutrophication, a part of the pond was separated by a dam. In 1990/91, in addition to the upper pond, a pre-treatment basin with gravel bars was set up, which was supposed to improve the quality of the water. In addition, particularly sensitive areas of the NSG were closed to visitors and provided with a fence