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Climate warming is predicted to affect northern lake food webs in two ways: (1)directly via changes in water temperature and ice conditions, and (2) indirectlyvia changes in catchment characteristics and processes that influence input ofallochthonous coloured dissolved organic matter (cDOM) and nutrients. Input ofcDOM increases carbon dioxide (CO2) availability, causes brownification andreduced light conditions, and may increase nutrient availability especially forpelagic primary producers. Increased water temperature and light penetrationand longer ice-free periods affect metabolic rates. These changes are expected toinfluence gross primary production (GPP) and growth of higher trophic levels.However, majority of studies focus on pelagic processes and net effects at wholelake scale is not well understood. Consequently, the lack of knowledge of whatfactors control benthic GPP makes predictions of net effects of climate change onwhole-ecosystem GPP spurious. The aim of this thesis was to experimentally testeffects of warming and increased input of allochthonous cDOM on habitatspecific and whole-ecosystem GPP in lakes. First, by manipulating the CO2concentrations in large scale pond ecosystems, we showed that increased CO2stimulated whole-ecosystem GPP. In a separate incubation study with naturallake sediments in a boreal lake, we tested the role of CO2 as a limiting factor forbenthic GPP under different light levels. The results showed that CO2 supplystimulated benthic GPP at high but not at low light availability, suggesting thatbenthic GPP can be CO2-limited. In the same experimental pond ecosystems, thecombined effect of increased allochthonous cDOM and warming (+3.5°C) on GPPwas studied. The results showed that cDOM input decreases whole-ecosystemGPP, mainly as a result of decreased benthic GPP due to light limitation not fullycounteracted by an increase in pelagic GPP under ambient conditions. Warmingon the other caused a hump shaped increase in whole-ecosystem GPP withincreasing cDOM input mainly due to a positive response in pelagic GPP due torelaxed nutrient limitation. Finally, by manipulating the fish consumer biomassin the same experimental pond ecosystems we showed that whole-ecosystem GPPcan be controlled by top-down effects under warm (+ 3.0°C) but not ambienttemperature conditions. The decline in whole-ecosystem GPP was mainlyattributed to a warming-stimulated consumer-driven trophic cascade in thepelagic habitat and top-down control by zooplankton on phytoplankton growth,while no corresponding cascade was evident in the benthic habitat.Taken together, the results suggest that climate change impacts, as increasinginputs of cDOM, warming and changes in food webs, have different effects onhabitat specific GPP and alone or in combination have impacts on whole-lakeGPP. This thesis offers important insights to better understand the factors thatcontrol lake GPP and to predict future lake ecosystem responses to environmentalchange.