Harmful algal blooms (HABs) are a global concern in both freshwater and coastal systems; creating dire consequences for public health, water resources, and local economies. Thus, there is a focus among scientists and environmental managers on HAB prediction, prevention, and mitigation. Current chemical mitigation methods include algicides such as copper sulphate, chlorination, and hydrogen peroxide, which can have high financial costs and secondary pollution associated with them. The use of natural allelochemicals produced by plants and bacteria has received considerable attention as an alternative to synthetic algicides, as they can have negligible toxins, be highly selective, and easily degraded in the environment. This dissertation is a coalition of research looking into new sources of plant allelochemicals and whether natural levels of allelochemicals in the water column, can impact phytoplankton communities and the presence of toxin-producing algal species. The first objective focused on the use of the waste product: brewer’s spent grain (BSG), as a new control mechanism to inhibit the growth of toxic algae. BSG extract of doses higher than 250mg/L inhibited the growth of freshwater and marine toxin-producing cyanobacteria and dinoflagellate species (Microcystis aeruginosa and Karenia brevis), while not impacting the diatom and chlorophyte tested (Scenedesmus obliquus and Prorocentrum tricornutum). This same dosage of BSG caused cyanobacteria abundance in lake water to decline by 90% within 4 days and chlorophytes to dominate the community by day 6 during a microcosm study. However, an experiment controlling bacteria levels demonstrated that the decline of K. brevis growth was likely due to the increase in abundance or presence of certain types of bacteria growing with exposure to BSG extract rather than due to chemicals released from the BSG. The second and third objectives shifted focus to the New Jersey Pinelands and whether the chemicals released into the water from terrestrial and marine plants in these waters, like phenolic compounds, impact the phytoplankton community and toxin-producing species. The second objective focused on the spatial and temporal distribution of phycotoxins along two New Jersey estuaries using passive samplers and whether the utility of passive samplers was impacted by the excess phenolic compounds in the water. By utilizing passive samplers in New Jersey, phycotoxins not previously reported in the area were described, such as azaspiracids, goniodomin-A and yessotoxins. However, this objective also showed some of the caveats of passive samplers, especially at sites with high phenolic compounds. The third objective focused on identifying the primary environmental drivers of chlorophyll a concentration and phytoplankton community along the freshwater – marine continuum of two New Jersey Estuaries with varying levels of disturbance. This dissertation explored BSG as a novel control method of HABs, and provided new information for monitoring, managing, and modeling HABs based on phenolic content measured in the water.