To understand the environmental factors affecting the spatiotemporal distribution of copepods, sampling was conducted seasonally in a small mesotidal inlet and estuary located in Doam Bay of southwestern Korea. The study area was divided seasonally into two or three station groups (estuarine, mixed, and coastal) by a cluster analysis and non-metric multidimensional scaling based on copepod abundance. Acartia forticrusa, A. hudsonica, A. ohtsukai, Paracalanus parvus s. l., Pseudodiaptomus marinus, Tortanus derjugini, T. dextrilobatus, T. forcipatus, Oithona spp., and harpacticoids were important species for grouping the stations. The spatiotemporal distribution of the first two species was restricted to the estuarine area in summer and significantly correlated with temperature, salinity, and chlorophyll-a concentration. The distribution of other brackish species, such as T. derjugini and T. dextrilobatus, significantly correlated with temperature, salinity, and chlorophyll-a concentration. In contrast, A. hudsonica significantly correlated with dinoflagellate density and turbidity in winter, in addition to the abovementioned environmental factors. Acartia hudsonica also maintained a large population in the estuarine area in fall and winter, and its distribution extended across the entire bay in spring. Other coastal species occurred in all areas and did not significantly correlate with environmental factors. Therefore, brackish species in the study area may have developed seasonally different behaviors to sustain their populations.