β-diversity has been frequently used in studies examining the degree of spatial variations in community structures. However, although it may be useful to quantify temporal variations of the communities, β-diversity is not much used for examining the variations along with time-course changes in a single community. In this study, to clarify if environmental factors causing the temporal variations vary depending on time scales, we examined the temporal β-diversity at various temporal scales for a zooplankton community in a small mountain lake where samplings were made for nine years. Analysis of the temporal β-diversity at various time scales with environmental variables showed that water temperature was a prime factor regulating the inter-seasonal variations of the zooplankton community structure but algal food conditions were more important in the intra-seasonal variations. Algal food conditions was also an important factor causing variations in the community structure in the same month but different years. The results clearly showed that environmental factors affecting the zooplankton community changes depending on the temporal scales examined. As such, temporal β-diversity is useful to quantify variations and relative importance among factors regulating the structure and species composition of plankton communities at various temporal scales.