Copepods are important secondary producers that support higher trophic levels in aquatic food webs. Large-scale climate events such as climate oscillations and global warming forcing on physical and chemical conditions in aquatic ecosystems might regulate zooplankton production through physiological and biochemical processes. We evaluated how large climatic and anthropogenic events impacted the secondary production of copepods in Lake Biwa, the largest lake in Japan. We determined food conditions and demographic traits such as body size, growth rate, biomass and production of the dominant warm-adapted copepod Eodiaptomus japonicus in this temperate lake, which experienced changes in trophic status and thermal regime over four decades (1966-2010). We firstly defined a size-based food index suggesting that this copepod continuously suffered from food shortages in this lake including the eutrophication period. The combined results of wavelet analysis and cluster analysis indicated that E. japonicus exhibited different seasonal cycles (unimodal and plurimodal) during the study period. The common unimodal seasonal cycle of the copepod was disrupted on several occasions during which it presented sometimes two or three modes. Wavelet coherence analysis revealed a strong stationary correlation with lake temperature for the demographic traits such as total abundance, clutch size and birth rate, but a transient correlation with the body size of females at the annual scale. Discriminant analysis between unimodal and plurimodal seasonal cycles highlighted the low temperature and high predation in leading to plurimodal cycles. Disruption of the short-term cycle of E. japonicus resulted mainly from the interaction and strength of bottom-up and top-down control rather than temperature. Long-term quasi-decadal periodicities (8 years) were also detected in the food index and demographic parameters such as growth and production for this copepod throughout the study period. These long-term periodicities were highly correlated with the Arctic Oscillation, implying that long-term trends in climate could regulate copepod food availability and production. This correlation weakened after 1990, which might be due to a regime shift in the lake environment induced by the rapid warming after the mid-1980s. Our results support the hypothesis that aquatic ecosystems subjected to global warming are less stable because of weakened causal interactions among ecosystem components, including nutrient cycling and plankton producers. Global warming might now be disrupting historical periodicity in secondary production in Lake Biwa.