Phytoplankton communities, with emphasis on picoplankton and nanoplankton, were investigated in Gamak Bay, South Korea, where freshwater input and coastal water intrusion shape ecosystem functions. Shellfish farms and fish farms are located in the inner bay and outer bay, respectively, and tides translocate uneaten food and urine production from aquaculture farms toward the inner bay. Water masses were distinctly different based on a significantly different density between the surface and bottom layer and among three water masses, including the inner bay, outer bay, and Yeosu Harbor. Phytoplankton communities were quantified using flow cytometry and size-fractionated chlorophyll-a (chl-a) was measured. Salinity was a principal variable separating phytoplankton communities between the surface and bottom layer, whereas Si(OH)4 controlled the communities in the inner bay, and NH4 + and PO4 3- governed the outer bay communities. While phycocyanin-containing (PC) cyanobacteria dominated in the outer bay, phycoerythrin-containing (PE) cyanobacteria dominance occurred with cryptophyte dominance, indicating that nutrients affected the distribution of pico- and nanoplankton and that cryptophytes potentially relied on a mixotrophic mode by feeding on PE cyanobacteria. Interestingly, picoeukaryotes and eukaryotes larger than 10 μm were mostly responsible for the ecological niche in the western region of the bay. Given that chl-a levels have historically declined, our study highlights the potential importance of increased small phytoplankton in Gamak Bay. Particularly, we urge an examination of the ecological role of small phytoplankton in the food supply of cultivated marine organisms.