Empounded in 1974, it was developed as part of a flood control project prompted by a particularly damaging tropical storm that hit the region downstream in September 1945.

[3] Originally authorized in 1963 as the New Hope Lake Project, the reservoir was renamed in 1974 in memory of B. Everett Jordan, former US Senator from North Carolina.

[6][7][8] Jordan Lake was declared as nutrient-sensitive waters (NSW) by the North Carolina Environmental Management Commission from 1983, the year it was impounded.

The rules were developed with extensive meetings, public hearings and negotiations between residents, environmental groups, local and state government agencies and other stakeholders.

[11][12] From July 2011 several NC laws have been passed delaying and weakening the rules, culminating in a plan to deploy floating arrays of in-lake circulators intended to reduce harmful algae and excessive chlorophyll.

On December 21, 2017, researchers at Duke University have discovered elevated levels of several perfluorinated compounds an unregulated family of industrial chemicals including some that can raise cancer risks in Jordan Lake and drinking water treated by the town of Cary.

Bald eagle habitat being endangered by trash submerged by the lake's creation spurred volunteer efforts to clean up the shoreline and other sensitive areas.