Following the cessation of private buses in Port Huron in 1968, BWAT commenced operations in 1976, with the assistance of neighboring SEMTA.

[3] BWAT began operating buses powered by compressed natural gas in 1996, and soon held the largest alternative-fuel transit fleet in Michigan.

December 2015 saw the opening of the Blue Water Transit Bus Center in downtown Port Huron, which serves as the system's main hub.

The $9.8 million facility includes a small store, as well as underground boilers to keep the sidewalks clear of snow and ice in the winter.

Numbered routes begin and end at the Blue Water Transit Bus Center downtown.