Harmful Algal Blooms (HABs) have been observed in all 50 states in the U.S., ranging from large freshwater lakes, such as the Great Lakes, to smaller inland lakes, rivers, and reservoirs, as well as marine coastal areas and estuaries. In 2014, a HAB on Lake Erie containing microcystin (a liver toxin) contaminated the municipal water supply in Toledo, Ohio, providing non-potable water to 400,000 people. Studying HABs is complicated as different cyanobacteria produce a range of toxins that impact human health, such as microcystins, saxitoxin, anatoxin-a, and cylindrospermopsin. HABs may be increasing in prevalence with rising temperatures and higher nutrient runoff. Consequently, new tools and technology are needed to rapidly detect, characterize, and respond to HABs that threaten our water security. A framework is needed to understand cyber threats to new and existing technologies that monitor and forecast our water quality. To properly detect, assess, and mitigate security threats on water infrastructure, it is necessary to envision water security from the perspective of a cyber-physical system (CPS). In doing so, we can evaluate risks and research needs for cyber-attacks on HAB-monitoring networks including data injection attacks, automated system hijacking attacks, node forgery attacks, and attacks on learning algorithms. Herein, we provide perspectives on the research needed to understand both the threats posed by HABs and the coupled cyber threats to water security in the context of HABs.