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Summary Ecosystem stability and regime shifts has become a central research topic in ecology and environment over the latest decade. Ponds and shallow lakes have been central to the development of the concept of alternative stable states and regime shifts in ecosystems. Ponds and shallow lakes can exhibit multistate stability and occasionally sudden transitions from regime to another. Since regime shift are common and frequently lead to severe ecological and economic losses, an increasing number of studies has suggested the need to detect the proximity to critical transition to prevent regime shifts. The first aim of this dissertation is to provide a better understanding of ecosystem stability in freshwater systems at different temporal scales, from among years to seasonal and weekly variation, and both within as well as among habitats. As a second aim, we also explore to what extent an evolutionary response can contribute to top-down control of algae and thus ecosystem stability. Our research used a combination of intensive field data collected in multiple consecutive years (2013, 2014, 2015, 2016 and 2017) and follow-up mesocosm experiment on resurrected Daphnia magna population. The findings from study can contribute to the debate on the occurrence of alternative stable state in freshwater system. Moreover, it provides a better insight on how evolution mediate ecosystem stability and functioning. In the first chapter we presented the difference in phytoplankton biomass (chlorophyll a concentration) with in and among years in a set of 25 fish ponds, and relate these difference to a variation in zooplankton body size and macrophyte cover. We found evidence that the 25 interconnected ponds differ strongly in their phytoplankton biomass and that these differences are associated with differences in nitrogen concentration, macrophyte cover in summer and zooplankton body size in spring. The differences in these characteristics among ponds result in repeatable differences in their state. Moreover, our results revealed that zooplankton grazing and macorphyte cover are important determinants for the variation in phytoplankton biomass. Chapter 2 reports a year to year turnover in environmental conditions and zooplankton community in the same set of ponds during three consecutive years. In this chapter we show the variation in environmental conditions and zooplankton community composition in the same set of ponds, we found repeatable differences among systems that are associated to pond management. Furthermore, environmental variables substantially varied among ponds and these differences are largely linked to the difference in fish pond management (Chapter 2). Chapter 3 focuses in to a higher temporal resolution data by monitoring chlorophyll a and phycocyanin loggers that were positioned in four neighboring ponds. In here, we quantify differences among years as well as among systems, and explore early-warning signals for sudden state shifts. In this chapter, we found a substantial variation in overall chlorophyll a as well as phycocyanin among years and systems. We also observed considerable variation within a year. We also show a strong association between chlorophyll a and phycocyanin, and found an indication of a regime shift in one pond in 2016. In chapter 4, We carried out a follow-up experiment on a resurrection ecology study that documented rapid adaptive change in a natural population of the water flea Daphnia magna in response to strong changes in fish predation pressure and study whether the observed genetic trait changes influence population dynamics and top-down control of phytoplankton. We conducted an outdoor mesocosm experiment in which we inoculated D. magna populations derived from three time periods of the same population known to have genetically adaptation to changes in predation pressure. Our results show that the interactions between adults and juveniles strongly impact the dynamics of populations and their top-down effect on algae and can be modulated by rapid evolution, such as here observed in response to changes in predation pressure.