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Many common and abundant copepods in coastal areas adapt to complex environments through diapause (physiological dormancy) by laying resting eggs. However, the response mechanisms of these species' phenology to environmental changes is poorly understood, especially the influence of both climatic and anthropogenic changes. Using monthly time series data for zooplankton in Tokyo Bay, Japan, from 1981 to 2010, we investigated phenological and quantitative changes in the dominant species Acartia omorii, Centropages abdominalis, and Labidocera rotunda in response to climatic and hydrographic variation in this semienclosed eutrophic coastal area. The first two species produce resting eggs in the warm season and the latter in the cold season. Decreasing abundance and increasing resting egg periods were observed for A. omorii and C. abdominalis, and the reverse for L. rotunda. Time series analysis revealed a possible mechanism driving these phenologic shifts. Wintertime warming of the water column associated with climate variability driven by the Pacific Decadal Oscillation index, followed by rapid development of summertime stratification and the formation of hypoxic bottom water layers, were responsible for the early initiation and delayed termination of the resting egg period for cold-water species. The warming trend in Tokyo Bay, possibly induced by inflow of warm oceanic water due to anthropogenic factors, caused these phenologic changes in the resting period and subsequently affected zooplankton abundance. These results suggest that the multiple stressors caused by climate change and other anthropogenic impacts can affect regional zooplankton communities in coastal areas.