The reserve has a history reminiscent of much of the northern part of the city.
When Māori lived in this area the extensive wetlands and easy access to the sea made the Styx an important area for mahinga kai (food gathering) and for the cultivation and harvesting of flax.
During European settlement the area was used for a number of purposes including sheep farming. The river was used to drive waterwheels and provided an important source of power for sawmills, flaxmills, and flourmills.
The Styx Mill Conservation Reserve area came into public ownership in the 1970s. Development began in the 1980s. Community involvement began with the Styx River Happening at Spencer Park in March 1999 and resulted in the formation of the Guardians of the Styx Charitable Trust. A sub-group researches the history of the river and its surrounding area, with a primary focus from 1850.