Remote sensing approaches that could identify species of submerged aquatic vegetation (SAV) and measure their extent in lake littoral zones would greatly enhance their study and management, especially if they can provide faster or more accurate results than traditional field methods. Remote sensing with multispectral sensors can provide this capability, but SAV identification with this technology must address the challenges of light extinction in aquatic environments where chlorophyll, dissolved organic carbon, and suspended minerals can affect water clarity and the strength of the sensed light signal. Here, we present environmental data collected to support a study using an unmanned aerial system (UAS)-enabled methodology to identify the extent of the invasive SAV species Myriophyllum spicatum (Eurasian watermilfoil, or EWM) in the Les Cheneaux Islands area of northwestern Lake Huron, Michigan, USA. Data collected includes water chemistry (nitrogen, phosphorus, carbon, suspended solids, chlorophyll a), light profiles, and submerged aquatic vegetation characteristics including cover, species dominance using aquatic vegetation survey methods (AVAS), and biomass.