Populations living in seasonal environments are exposed to systematic changes in physical conditions that restrict the growth and reproduction of many species to only a short time window of the annual cycle. Several studies have shown that climate changes over the latter part of the 20th century affected the phenology and population dynamics of single species. However, the key limitation to forecasting the effects of changing climate on ecosystems lies in understanding how it will affect interactions among species. We investigated the effects of climatic and biotic drivers on physical and biological lake processes, using a historical dataset of 40 years from Lake Washington, USA, and dynamic time-series models to explain changes in the phenological patterns among physical and biological components of pelagic ecosystems. Long-term climate warming and variability because of large-scale climatic patterns like Pacific decadal oscillation (PDO) and El Niño–southern oscillation (ENSO) extended the duration of the stratification period by 25 days over the last 40 years. This change was due mainly to earlier spring stratification (16 days) and less to later stratification termination in fall (9 days). The phytoplankton spring bloom advanced roughly in parallel to stratification onset and in 2002 it occurred about 19 days earlier than it did in 1962, indicating the tight connection of spring phytoplankton growth to turbulent conditions. In contrast, the timing of the clear-water phase showed high variability and was mainly driven by biotic factors. Among the zooplankton species, the timing of spring peaks in the rotifer Keratella advanced strongly, whereas Leptodiaptomus and Daphnia showed slight or no changes. These changes have generated a growing time lag between the spring phytoplankton peak and zooplankton peak, which can be especially critical for the cladoceran Daphnia. Water temperature, PDO, and food availability affected the timing of the spring peak in zooplankton. Overall, the impact of PDO on the phenological processes were stronger compared with ENSO. Our results highlight that climate affects physical and biological processes differently, which can interrupt energy flow among trophic levels, making ecosystem responses to climate change difficult to forecast.