An increase of dissolved organic carbon (DOC) in inland waters has been reported across the northern temperate region but the effects of this on whole lake ecosystems, often combined with other anthropogenic stressors like nutrient inputs and warming, are poorly known. The effects of these changes on different component of the ecosystem were assessed in an experiment using twenty-four large (3000L) outdoor mesocosms simulating shallow lakes. Two different temperature regimes (ambient and ambient +4 °C) combined with three levels of organic matter (OM, added as filtered peaty water), simulating the DOC increase that is predicted to take place over the next 4 to 21 years were used. Neither temperature nor OM had significant effects on net ecosystem production, respiration or gross primary production. Phytoplankton chlorophyll a concentration was not significantly affected by warming, however in summer, autumn and winter it was significantly higher in mesocosms receiving intermediate OM levels (July-Feb DOC concentrations 2-6 mg L-1). Summer cyanobacterial blooms were highest in intermediate, and lowest in the highest OM treatments. OM concentration also influenced total macroinvertebrate abundance which was greater in spring and summer in mesocosms with intermediate and high OM. Fish abundance was not significantly affected by OM concentration, but abundance was greater in ambient (55 fish subsample-1) compared to heated mesocosms (17 fish subsample-1) and maximum abundance occurred two weeks later compared to heated mesocosms. The results suggest that changes in OM may have a greater effect on shallow lakes than temperature and that phytoplankton, especially cyanobacteria, benefit from intermediate OM concentrations, therefore, nuisance algal blooms might increase in relatively clear shallow eutrophic lakes where DOC concentrations increase.