The California Current System is a diatom-dominated region characterized by seasonal coastal upwelling and additional elevated mesoscale activity. Cyclonic mesoscale eddies in the region trap productive coastal waters with their planktonic communities and transport them offshore with limited interaction with surrounding waters, effectively acting as natural mesocosms, where phytoplankton populations undergo ecological succession as eddies age. This study examines diatom community composition within two mesoscale cyclonic eddies that formed in the same region of the California Current System 2 months apart and in the California Current waters surrounding them. The diatom communities were analyzed in the context of shifting environmental gradients and through a lens of community succession to expand our understanding of biophysical interactions in California Current System cyclonic eddies. Diatom communities within each eddy were different from noneddy communities and varied in concert with salinity and dissolved iron (Fe) concentrations. The younger, nearshore eddy displayed higher macronutrient and dissolved Fe concentrations, had higher values for diatom Shannon diversity and evenness, and had nutrient ratios indicative of either eventual silicic acid (Si) or Fe limitation or possibly co-limitation. The older, offshore eddy displayed low macronutrient and dissolved Fe concentrations, was likely nitrate-limited, and had lower diatom Shannon diversity and evenness indices. Sequences from the genus Rhizosolenia, some of which form vertically migrating mats to bypass nitrate limitation, dominated in the older eddy. This is of potential significance as the prevalence of Rhizosolenia mats could impact estimates of carbon cycling and export in the wider California coastal area.Author Contributions Statement: C.P.T., P.D.C. and S.C. designed the underway sampling plan while P.D.C. and Z.M.A. conceived of the diatom community analysis plan. All authors contributed to sample processing and analysis of data. Z.M.A. and P.D.C. wrote the initial draft of the manuscript though all authors contributed substantially to editing of the manuscript and have approved the final submitted manuscript.