The timing of biological events, known as phenology, plays a key role in shaping ecosystem dynamics, and climate change can significantly alter these timings. However, few studies provide evidence of these effects in marine systems. The Gulf of Maine (GoM) on the Northeast U.S. Shelf is vulnerable to warming temperatures and other climate impacts, which could affect the distribution and production of plankton species sensitive to phenological shifts. In this study, we apply a multifaceted, data-driven statistical modeling approach to understand the population variability of Calanus finmarchicus, a lipid-rich copepod that is fundamental to the GoM food web. Our results reveal how phenology impacts the complex intermingling of top-down and bottom-up controls. Our findings suggest that early initiation of the annual phytoplankton bloom prompts an early start to the reproductive season  for populations of C. finmarchicus in the inner GoM, resulting in high spring abundance. This spring condition leads to enhanced predation pressure later in the season, consequently resulting in overall low C. finmarchicus abundance in the fall. These biologically controlled dynamics are less pronounced in the outer GoM, where water exchanges near the boundary have a greater influence. Our analysis augments existing hypotheses in fisheries oceanography and classical ecological theory by considering unique plankton life-history characteristics and shelf sea dynamics.