New technologies enable the opportunity to improve our monitoring and understanding of marine phytoplankton communities. However, careful consideration for how different methodological approaches, or 'lenses', influence our interpretation of phytoplankton ecology is important, particularly when drawing conclusions about change over time or space. Using both high-throughput 18S rRNA gene sequencing and microscopy, we explored how phytoplankton community structure varied over the course of a year within a nearshore semi-enclosed coastal embayment along the Central Coast of California. The seasonal shift in the relative community dominance (i.e., diatom vs. dinoflagellate dominance) was captured in the microscopy results but not effectively captured in the molecular-based findings. However, the molecular approach explained more of the variability in composition across seasons relative to the microscopy approach. Temporal dynamics of specific bloom-forming taxa also differed between the molecular and microscopy results. Overall, the observed differences between the molecular-and microscopy-derived characterization of phytoplankton dynamics suggest that the approaches are best suited to answer different research questions. Moreover, the approaches complement each other for a more comprehensive perspective of a coastal phytoplankton ecosystem. Therefore, identifying the biases of each approach within natural communities is necessary to effectively and accurately characterize phytoplankton communities.