Blooms of domoic acid (DA)-producing Pseudo-nitzschia diatoms are increasing in frequency and magnitude in California coastal oceans. Moreover, the molecular drivers and physical dynamics of such blooms are challenging to characterize. While work on bloom characterization is ongoing, little is known about the chemical landscape of the California coastal ocean where Pseudo-nitzschia blooms occur near-annually. This dissertation describes and employs multiple omics methods to understand Pseudo-nitzschia dynamics in the ocean and provides a greater understanding of the metabolomic composition of coastal California oceans during the spring and summer seasons when Pseudo-nitzschia blooms occur.Chapter 1 reviews the progress and challenges in using non-targeted metabolomics for aquatic chemical ecology. Chapter 2 identifies ocean depth and nutrient limitation as influencers of unique metabolome profiles in coastal California. Chapter 3 characterizes molecular mechanisms underpinning a toxic Pseudo-nitzschia bloom, improves forecasting for DA, and rationalizes the escalating prevalence of toxic Pseudo-nitzschia blooms. Chapter 4 studies the molecular mechanisms behind a low-toxicity Pseudo-nitzschia community, and identifies physical conditions associated with elevated expression of the first biosynthetic gene in the DA pathway. Chapter 5 provides insights into the breadth of jasmonic acid in the oceans and discovers that its presence alters the growth and metabolism of marine microorganisms. Together, these chapters highlight multi-omics methods to gain a deeper understanding of marine microbial communities, marine ecology, and applications to protecting public health.