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Global records of temperature show a warming trend both in the atmosphere and in the oceans. Current climate change scenarios indicate that global temperature will continue to increase in the future. The effects will however be very different in different geographic regions. In northern Europe precipitation is projected to increase along with temperature. Increased precipitation will lead to higher river discharge to the Baltic Sea, which will be accompanied by higher inflow of allochthonous organic matter (ADOM) from the terrestrial system. Both changes in temperature and ADOM may affect community composition, altering the ratio between heterotrophic and autotrophic organisms. Climate changes may thus have severe and complex effects in the Baltic Sea, which has low species diversity and is highly vulnerable to environmental change. The aim of my thesis was to acquire a conceptual understanding of aquatic food web responses to increased temperature and inputs of ADOM. These factors were chosen to reflect plausible climate change scenarios. I performed microcosm and mesocosm experiments as well as a theoretical modeling study. My studies had a holistic approach as they covered entire food webs, from bacteria and phytoplankton to planktivorous fish. The results indicate a strong positive effect of increased temperature and ADOM input on the bacterial community and the microbial food web. However, at the prevailing naturally low nutrient concentrations in the Baltic Sea, the effect of increased temperature may be hampered by nutrient deficiency. In general my results show that inputs of ADOM will cause an increase of the bacterial production. This in turn can negatively affect the production at higher trophic levels, due to establishment of an intermediate trophic level, consisting of protozoa. However, the described effects can be counteracted by a number of factors, as for example the relatively high temperature optimum of fish, which will lead to a more efficient exploitation of the system. Furthermore, the length of the food web was observed to be a strong regulating factor for food web responses and ecosystem functioning. Hence, the effect of environmental changes may differ quite drastically depending on the number of trophic levels and community composition of the system. The results of my thesis are of importance as they predict possible ecological consequences of climate change, and as they also demonstrate that variables cannot be examined separately.