Estuaries are key reactive ecosystems along the land–ocean aquatic continuum, with significant ecological and economic value. However, they have been facing strong morphological management changes and increased nutrient and contaminant inputs, possibly leading to ecological problems such as coastal eutrophication. Therefore, it is necessary to quantify the import and export fluxes of the estuaries, their retention capacity, and estuarine eutrophication potential. The 1-D Carbon-Generic Estuary Model (C-GEM) was used to simulate the transient hydrodynamics, transport, and biogeochemistry for estuaries with different sizes and morphologies along the French Atlantic coast during the period 2014–2016 using readily available geometric, hydraulic, and biogeochemical data. These simulations allowed us to evaluate the budgets of the main nutrients (phosphorus – P; nitrogen – N; silica – Si) and total organic carbon (TOC), and their imbalance, providing insights into their eutrophication potential. Cumulated average annual fluxes to the Atlantic coast from the seven estuaries studied were 9.6 kt P yr−1, 259 kt N yr−1, 304 kt Si yr−1, and 145 kt C yr−1. Retention rates varied depending on the estuarine residence times, ranging from 0 %–27 % and 0 %–34 % to 2 %–39 % and 8 %–96 % for total phosphorus (TP), total nitrogen (TN), dissolved silica (DSi), and TOC, respectively. Large-scale estuaries had higher retention rates than medium and small estuaries, which we interpreted in terms of estuarine residence times. As shown by the indicator of eutrophication potential (ICEP), there might be a risk of coastal eutrophication, i.e., the development of non-siliceous algae that is potentially harmful to the systems studied due to the excess TN over DSi. This study also demonstrates the ability of our model to be applied with a similar setup to several estuarine systems characterized by different sizes, geometries, and riverine loads.