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Water temperature controls the physiology, growth rate, distribution, and behavior of most plankton populations in the sea and thus affects the energy transfer in marine ecosystems. The present study focuses on the influence of seasonal changes in sea surface temperature on phytoplankton and the size distribution of copepods in the Arraial do Cabo Upwelling System (Brazil), where a wind-driven coastal upwelling can lead to multiple distinct bottom-up cascade effects on the food web. To address the potential effect of the seasonal changes, environmental data were obtained and the abundance of plankton determined from monthly samples collected in triplicate from 2010 to 2014. The samples were analyzed on a Benchtop FlowCAM (FC), and copepods (<1000 µm) were classified according to their Ellipses Equivalent Major Axis using image analysis software ImageJ (IJ). For IJ analysis, a batch-processing macro was built to open all FC raw images and then crop each copepod individually into a single picture. Using these images, prosome and urosome lengths were manually measured with the straight-line tool in IJ. With the combinations of measurements obtained in the IJ adjusted as FC measurements, we established a new, faster, and more effective way to measure copepods. With the copepod size classification, we found that there is a cycle in copepod size combined with the upwelling cycle that is related to temperature rather than to phytoplankton growth. Copepod abundance as a whole peaked during the autumn, winter, and spring seasons. The method performed here proved that FC is an effective tool for classifying copepod sizes and detecting seasonal variation. [ABSTRACT FROM AUTHOR]