Unmanned aerial vehicles (UAV) are increasingly being used in water supply infrastructure inspection, resulting in a large volume of aerial visual assets (static photographs or videos). How to efficiently extract water channels from such assets for the benefits of hazard detection remains a challenge. This paper provides an aerial video processing approach for the extraction of various water channel structures, which includes a main algorithm based on the registration of video frames into a building information model (BIM), and a complementary algorithm enabled by aerial video spatio-temporal continuity. Experimental results demonstrate the effectiveness of the proposed approach, which can reliably extract water channels with least manual intervention. The results reveal the promise of exploiting readily-available information from BIM to automate aerial video processing. Future research is suggested to further explore the generalizability of the approach concerning variant flight settings and external environments.