In the late 1800's the popularity of fly-fishing in the Cape Colony gained so much momentum that a need was identified for a breeding program for trout to stock local rivers and dams. This led to the establishment of a trout hatchery in the picturesque Jonkershoek Valley, eight kilometers outside Stellenbosch in the Western Cape. A hatching house, as well as ten fishponds, were built by the hatchery's first curator, Mr. John Scott. It was here that the first trout was successfully bread in South Africa in 1893. The facilities of the hatchery were greatly expanded in 1943 with the addition of another 15 ponds next to the Eerste River. The hatching program was also expanded to include indigenous fish species.

In subsequent years the hatching program was substantially scaled down and many of the hatchery's ponds became redundant and fell into ill repair. In 2001 the Western Cape Nature Conservation Board, who owns the premises, decided to award a tender to have the dams repaired and operated as a fly-fishery on a concession basis. This concession gave birth to Jonkershoek Fly-Fishing.

The enormous task of repairing century-old fishponds, that were built to accommodate a hatchery, and turning them into a premier fly-fishery began in January 2002. For five months a dedicated team of six men worked side by side with heavy earth moving equipment to turn these silted-up ponds into a fly-fishery. Holes in pond walls large enough to drive a truck through were repaired, dead trees were removed, damaged trees were pruned, race ways that were unused for twenty years were cleaned (in some cases rediscovered!) and ponds were shaped and merged where necessary. In June 2002 Jonkershoek Fly-Fishing opened its doors, or should that be ponds, to the public.

The historical hatchery, which is a National Monument today, is still producing trout every year and is operated by the Aqua-culture Division of the Stellenbosch University. The hatchery forms part of their research and educational facility for students in aquaculture.