Invasive submerged aquatic vegetation (SAV) such as Hydrilla verticillata and influxes of excessive nutrients drastically alter the composition of primary producers in aquatic systems, creating unique challenges for managers. Avian vacuolar myelinopathy (AVM) is an often-lethal disease affecting waterbirds and raptors linked to a neurotoxin-producing epiphytic cyanobacterium (Order Stigonematales; stig) that grows primarily on invasive SAV. Managers have difficulty reducing loss of avian wildlife to AVM due to the difficulty of detecting stig in systems prior to an outbreak; additionally, the only current management option is the complete removal of SAV. We developed proximal hyperspectral remote sensing methods to rapidly detect the presence of stig on SAV. Additionally, we evaluated the use of algaecides as a management strategy to reduce the presence of stig. Of the algaecides tested, none proved to be effective at reducing the presence or density of stig on hydrilla leaflets in field or laboratory trials.