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 a and 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.