Our society has become more and more dependent on natural ecosystems while, at the same time, putting more pressure on it than ever. In order to use these ecosystems in a sustainable way, we need to understand how they work on a fundamental level. Freshwater ecosystems are complex with many interacting drivers and factors. These include biotic factors, such as phytoplankton and other organisms such as grazers and parasites. Furthermore, the dynamics in freshwater ecosystems are driven by the interactive effects of abiotic factors such as temperature, light and nutrients on biotic factors. One of the topics that has been neglected for a long time, and is still understudied is how parasites and phytoplankton interact. I studied how the effects of abiotic factors interact to shape the dynamics between cyanobacteria and chytrid parasites. In order to study the effects of multiple factors and their interaction, it is necessary to run large multi-factorial experiments. To this end, I developed a method to measure the biovolume of filamentous phytoplankton in semi-automated manner fast and reliably (Chapter 2). In chapter 3 I investigated how P. rubescens-chytrid dynamics were affected by the interactive effects between temperature and light. Furthermore, I adapted an existing dynamical model to examine the long-term effects of temperature and light on the dynamics between host and parasite. This has shown that increased temperature and light leads to conditions were P. rubescens can grow, but it is much affected by chytrid infection leading to cycles of growth and decline of both the host and the parasite. Chapter 4 is a follow-up of the experiment done in chapter three with the inclusion of varying phosphorus concentrations in addition to temperature and light. Here I show that only at low temperature, there is an effect of the phosphorus treatment on the infection by chytrids. Chytrids otherwise are able to infect P. rubescens filaments with low C:P ratios that have been brought on by phosphorus limitation. During the work on this thesis, we also managed to isolate a new species of chytrids, that only infects heterocyst cells of D. planktonicum. In chapter 5 we performed an experiment to assess the effect of chytrid heterocysts infection on D. planktonicum growth and nitrogen fixation. The results show that under nitrogen deficient conditions, D. planktonicum cannot sustain growth when and total nitrogen fixation is reduced 14-fold because of chytrid heterocysts infection. This signifies a potential important effect of parasitism on the nitrogen cycle in lakes. This thesis contributes to a better fundamental understanding of how different environmental factors interact to shape parasite-host processes in aquatic ecosystems. We show that P. rubescens becomes more vulnerable to chytrid infections with increases in temperature and light, offering an alternative biological explanation for the specific niche of P. rubescens. Host C:P ratios have furthermore only limited effect on chytrid infections, dependent on temperature. We show that potentially, chytrids indirectly utilize light while their host is still alive, and that chytrids infecting heterocysts likely make use of the inherent transport of metabolites between heterocysts and vegetative cells. Evidently the interaction between effects of abiotic and biotic factors are important to gain a fundamental understanding of aquatic ecosystems and how they function.