Eutrophication, the excess nutrient input to marine systems, can intensify harmful algal blooms (HABs) and contribute to ecosystem stressors such as hypoxia and ocean acidification. Along the U.S. West Coast, blooms of Pseudo-nitzschia spp. (PN), producers of the neurotoxin domoic acid (DA), pose risks to ecosystems, human health, and coastal economies. Understanding how natural and anthropogenic nutrient sources influence bloom dynamics is essential to assess ecosystem vulnerability and inform coastal management. This dissertation investigates the physical and biogeochemical drivers of PN HABs along the California coast, focusing on terrestrial nutrient inputs and their impacts on bloom intensity, toxin production, and co-occurring stressors.Chapter 1 outlines the scientific context and research questions, synthesizing prior work on eutrophication and HABs in the region. Chapter 2 uses a 20-year observational dataset to analyze spatial and temporal patterns of PN HABs across three hotspots: Monterey Bay, Santa Barbara Channel, and San Pedro Channel. Coastwide, DA events are linked to upwelling intensity, elevated chlorophyll-a, and silicic acid limitation. However, regional differences emerge—Monterey Bay events often occur under nutrient-poor, low-upwelling conditions, while PN blooms in the Santa Barbara and San Pedro Channels are associated with colder, nitrogen-rich waters. Chapter 3 implements a mechanistic DA production model within a three-dimensional hydrodynamic-biogeochemical framework for the Southern California Bight. Simulations show that anthropogenic nutrient inputs shift nutrient limitation from nitrogen to silica, enhancing DA production and increasing surface pDA by ~25%. Chapter 4 expands this modeling approach to the San Francisco–Monterey Bay region, incorporating nutrient inputs from rivers, wastewater, and San Francisco Bay. Terrestrial inputs increase coastal nitrogen by 11.4%, primary production by 6.5%, and chlorophyll by 4.5%, raising the likelihood of HAB-favorable chlorophyll concentrations by 10–45%. Declines in oxygen and pH are more localized. Chapter 5 synthesizes findings, emphasizing the importance of including terrestrial nutrient sources in predictive HAB models and ecosystem management strategies. The results highlight the value of integrated modeling for understanding and mitigating coastal biogeochemical change under increasing human and climate pressures.