The growing field of aeroecology is limited by difficulties associated with sampling in the air column. Aerial insects are particularly hard to sample, despite being the main prey in the air column, with some recent studies attempting to use drones as a collection method. We conducted a study to determine the optimal drone settings for collecting insects above the canopy, where drones are seldom used. By attaching a net to the body of a small, commercial drone, we tested yield from different height, speed, and net settings in wetlands, as well as compared insect diversity across different habitat canopies. Height was the most important setting; grazing the canopy yielded significantly more insects than flying one meter above it. Speed, drone type, and net size did not influence the number of insects caught per trial. Wetland canopies had higher abundance, diversity, and species richness in its arthropod populations compared to forest canopies or lakes. Compared to the yield of Lindgren funnels—a traditional sampling method in entomology—drones captured higher diversity and abundance of insects in a fraction of the time. This study confirms that drones are an efficient and accurate way to collect canopy arthropods.