Regime shifts in shallow lakes are typically characterized by submerged macrophyte (clear water regime) or phytoplankton (turbid regime) dominance. Climate warming is expected to affect water quality and facilitate turbidity in lakes, but we may also expect synergistic effects on organisms' interactions from climate and local specific dynamics in lakes. We here examined long-term changes in phytoplankton composition in July and August from 1980 to 2011 in a temperate shallow lake, Lake Krankesjon, a dataset including 21 years throughout a 31-year period. We hypothesize that although effects of the ongoing climate change are visible in our long-term data set, local specific dynamics override climate effects. We found that cyanophytes were the most abundant phytoplankton taxa among which small-sized colonial cyanobacteria were dominant. Both population density of small-sized colonial cyanobacteria and maximum water temperature increased over the period of study. However, the variations in the phytoplankton assembly were likely mainly related to three principal factors, including the local availability of nutrients, grazing from zooplankton, and possibly, an increasing trend in temperature. The first two factors are associated with the local specific dynamics, while the last with regional climate. Our long-term study showed that although there were potential climate warming effects on the phytoplankton community, local factors, such as biotic interactions and nutrient availability, were likely stronger drivers than climate warming in Lake Krankesjon at least over the last 30-year period.