Climate change brings many environmental changes over the world and the effects of the climate change have a major impact all ecosystems. These effects pose a threat to the brackish Baltic Sea in Europe. In the Baltic Sea the water temperature is rising, the ice cap is shrinking, and the northern region of the sea average annual precipitation is increasing, leading to more nutrients such as nitrogen and phosphorus being added to the system. Climate change will affect aquatic ecosystems in several ways, including changes in distribution, phenology, increased risk of ecosystem collapse and extinction caused by, for example, increased water temperatures and changes in water chemistry. Different species are expected to react to these changes in different ways and at different rates. In this study, zooplankton was investigated, with a main focus on copepods and how their annual cycles were affected by climate change. Copepods were taken from sites that have experienced 50 years of warmer temperatures due to cooling water discharges from a nuclear power plant within the sampling area. These samples were compared to a control bay that had a normal temperature in relation to the season. The study investigated whether long-term warming has led to altered reproductive patterns with overwintering populations in the warm bay as opposed to an annual cycle where winter is avoided through the production of dormant eggs. Temperature, chlorophyll a and water samples for phytoplankton, DNA analyses and zooplankton abundance were compared between the two bays. The results showed a significant difference between the bays, both in the composition of the zooplankton community over time and occurrence. Warmer temperatures appear to have favoured the abundance of Acartia spp. and a change in phenology was seen within the species in the warm bay as they showed an earlier emergence in spring associated with an increase in chlorophyll a and an advanced phytoplankton bloom. Eurytemora spp. were found in greater numbers during the winter months in the control bay. This may indicate that the two species exhibit different phenologies and have species-specific differences in temperature optima. Other species in these waters showed no clear signs of altered phenology. Among other zooplankton found was Balanus. This species was only found in the warm bay and was therefore considered a heat favoured species. Based on the results, it cannot be said with certainty whether copepods in the warm bay have stopped producing dormant eggs, but it does show that these individuals have shifted their annual cycle forward over time. With a warmer future climate, the ability to respond to changes in the timing of phytoplankton blooms may differ among zooplankton species. It is possible that more species such as Acartia spp. will dominate these waters, out- competing the less heat-tolerant species such as Eurytemora affinis. To some extent, copepods may change their life cycle with increasing temperature and advanced algal bloom, and thus there is a chance to exclude the overwintering stage. Diapause transports a large amount of carbon, therefore changes in diapause phenology in connection with climate change can have a major impact on ecosystems and the climate. Whether or how zooplankton species will adapt to continued climate change will be decisive for the effects on ecosystems in all waters.