With the recent rise in harmful algae blooms (HABs) events in the Finger Lakes region, it is imperative to develop efficient means to identify, track, and predict blooms. Aerial imaging has proven increasingly applicable as an environmental research tool as camera, spectrometers and drone technologies advance. Challenges for monitoring HABs: (1) Blooms are transient phenomena (2) Thousands of algal bloom species co-exist with other constituents in the water body (sediments, and dissolved organic matter) (3) Presence of other constituents obscures signature of algal blooms. (4) Calibration and quantifying output sensor data. This project focuses on investigation of HABs using spectrometers, optical and multispectral camera mounted on unmanned aerial systems (UAS). From these imagery and in-situ data we hope to generate a correlation between aerial images and HABs concentration.