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Estuarine ecosystems play a crucial role in global carbon cycling. Understanding the factors controlling plankton metabolism in these regions is critical. This study investigates how contrasting nutrient conditions influence plankton metabolism and carbon flow in two Danish estuaries, Roskilde Fjord (RF) (eutrophic) and the Great Belt (GB) (less eutrophic). Despite higher nutrient concentrations in RF, chlorophyll aand biomass only showed a moderate increase compared to the GB. Interestingly, metabolic rates (photosynthesis and respiration) in RF displayed greater temperature sensitivity, suggesting potential nutrient limitation effects in the GB. While both stations exhibited similar annual net primary production, RF's higher net community production highlights the importance of nutrient availability for carbon accumulation within the system. Additionally, the study observed significant seasonal variations in plankton metabolism and its impact on the carbon cycle. Notably, the more dynamic hydrography in the GB weakened correlations between biological and environmental factors. All seawater is full of microscopic organisms known as plankton. Plankton play a central role in controlling the global carbon cycle and phytoplankton is the marine counterpart to land‐based plants. Phytoplankton harness sunlight and available nutrients from their environment, to take up carbon dioxide from the atmosphere and produce food and oxygen. Our study investigated how plankton change their activities over a year in two different coastal waters of Denmark in the Baltic Sea. We tried to understand how the differences in both the biological differences within the plankton, which are at the bottom of the food web, and the differences in their food sources affect their metabolism, both by conducting measurements in the sea and by applying experiments on the samples taken. Based on the available information, the Roskilde Fjord (RF), with a depth of 5 m, has slow water movement and is more exposed to fertilizers. This leads to more plankton and increased sensitivity to temperature changes compared to the Great Belt, an open sea with faster water flow. Areas with higher nutrient levels, like the RF, are expected to be more affected by rising sea temperatures due to climate change. Plankton metabolism responds rapidly and efficiently to biogeochemical and seasonal changes, making it vulnerable to anthropogenic effectsTrophic dominancy in the community respiration varies with the quality and quantity of the carbon sourceThe mixing zone of both stations was estimated to be net autotrophic, which provides carbon to upper trophic levels Plankton metabolism responds rapidly and efficiently to biogeochemical and seasonal changes, making it vulnerable to anthropogenic effects Trophic dominancy in the community respiration varies with the quality and quantity of the carbon source The mixing zone of both stations was estimated to be net autotrophic, which provides carbon to upper trophic levels