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• A 3.5 °C warming of lake has marginal effect on dissolved CO 2 and CH 4 concentrations. • Monthly temperature and nutrient changes drive seasonal lake water carbon. • The dependence of CO 2 and CH 4 on temperature and nutrients is different. • The temperature threshold affecting aqueous CO 2 is likely to be around 9 °C. Shallow lake ecosystems are highly sensitive to temperature fluctuation because of their high water surface-to-volume ratios. Shallow lakes have been increasingly identified as a hotspot of CO 2 and CH 4 emissions, but their response to temperature variation remains unclear. Here, we report from a 5-month outdoor mesocosm experiment where we investigated the impacts of a projected 3.5 °C future warming and monthly temperature changes on lake CO 2 and CH 4 , as well as the key drivers affecting the lake carbon cycling. Our results show that CO 2 and CH 4 concentrations had a significantly positive correlation with monthly temperatures. CH 4 concentration was primarily regulated by monthly temperature, while nutrients effects on CO 2 concentration overrode climate warming and temporal temperature changes. These findings imply the varied roles that temperature and nutrient levels can play on CO 2 and CH 4 dynamics in shallow lake systems. The relationship between temperature and CO 2 concentration was nonlinear, showing a threshold of approximately 9 °C, at which CO 2 concentration could be strongly modified by nutrient level in the lake systems. Understanding this complex relationship between temperature with CO 2 and CH 4 concentrations in shallow lakes is crucial for effective lake management and efficient control of greenhouse gases (GHGs) emissions. [Display omitted] [ABSTRACT FROM AUTHOR]

• Nitrogen addition effect overrides warming effect on p CO 2 in shallow lakes. • Interplay of warming and nitrogen addition causes the mesocosms from a CO 2 sink to a weak CO 2 source. • Warming and nitrogen addition collectively change phytoplankton community structure. • Bacillariophyta may be a useful biological indicator for predicting aqueous p CO 2. Shallow lakes are numerous in all climate zones, but our knowledge about their dissolved carbon dioxide (CO 2) response to future climate change and nutrient enrichment is rather limited. Here we performed a mesocosm experiment with four treatments to investigate how warming and nitrogen addition will impact the partial pressure of CO 2 (p CO 2) and phytoplankton community individually and combined. We found that warming alone had no significant effect on p CO 2 , while nitrogen addition increased p CO 2 significantly. The combined effects of nitrogen addition and warming on p CO 2 level were prevalent, indicating that eutrophic shallow lakes would be double-jeopardized in the future climate. Warming and nitrogen addition together also showed to have changed the phytoplankton community structure, suggesting a potential shifting of biological system in shallow lakes under changing climate. These findings highlight the importance of reducing nitrogen pollution to shallow lake systems for sustainable development goal. [Display omitted] [ABSTRACT FROM AUTHOR]