Ground truth data collection in bodies of water traditionally relies on the use of watercraft and manual sampling. The transport and cost associated with the use of this type of equipment, as well as the time required to reach the site of collection, may all be significantly reduced by the use of small unmanned aerial vehicles (UAV) or drones. In this project we evaluate the implementation of a modified UAV with the ability to collect a small volume of surface water up to 400m offshore. The bacterial flora found in the water of several locations in the Lake Ontario-Rochester Embayment area is then entered into a multi-year database that attempts to correlate hyperspectral data obtained by the Landsat 8 Operational Land Imager with the isolated bacterial species. We found that water collection using a consumer grade UAV facilitated sampling efforts, saving time and providing easy access to otherwise difficult to reach collection sites