Mesoscale eddies are fundamental drivers of physical and biological variability in the ultra-oligotrophic Southeastern Mediterranean Sea (SEMS). By integrating two long-term satellite altimetry datasets (DYNED and PET, 1993–2025), this study characterizes the seasonal spatiotemporal dynamics of cyclonic (CE) and anticyclonic (ACE) eddies and assesses their ecological impacts on phytoplankton biomass. Our analysis reveals polarity-based dynamics, though several physical metrics are sensitive to eddy-detection method: ACEs showed a tendency toward longer lifetimes than CEs, rotational velocity rankings reversed between datasets, and CEs consistently dominated high-density spatial hotspots. Seasonal patterns indicate peak eddy activity between February and April, followed by a basin-wide decline during the summer months. Our investigation of surface chlorophyll-a (Chl <em>a</em>) distributions challenges the classical "productive oasis" paradigms; most CEs demonstrate negative Chl <em>a</em> anomalies and depleted cores, potentially driven by intense top-down grazing pressure. Conversely, ACEs encompass larger areas of influence and may therefore facilitate greater horizontal retention, producing a larger area-integrated surface Chl <em>a</em> footprint and potentially supporting greater phytoplankton biomass through bottom-up nutrient accumulation. Our findings suggest that mesoscale features in the SEMS function as active ecological mechanisms, restructuring the basal food web via differential transport, retention, and community succession. This work emphasizes the need for coupled physical-biological frameworks to understand ecosystem resilience in nutrient-impoverished basins facing global climate change.