Freshwater reclaimed marshes along the European Atlantic coast are highly suitable for European eels (Anguilla anguilla). However, European eel stocks have declined, and the coastal marshes have been subjected to major disturbances. The objective of our study was to analyze the processes governing patterns of European eel microhabitat distribution of four eel size classes (from <160 mm to >360 mm) in a reclaimed marsh (France). Analyses were conducted using artificial neural network (ANN) techniques and ecological profiles. Our ANN results showed that eel densities were significantly related to three major influencing variables: the width of ditch section, the silt depth, and the density of emergent plants. Such ecological profiles were significantly different between small (<240 mm) and large eels (>360 mm): small eels were more widespread than large eels. Large eels were absent or at low densities in shallow ditches with a high aquatic plant cover obstructing the water column and a large quantity of silt. These characteristics seem to define the ditches not directly connected with the main river where dredging operations were rare. Management of regular dredging operations in the channels by maintaining a mosaic of permanent aquatic habitats and avoiding the heavy silt loads in most ditches should be promoted. This dredging operation was probably one of the most promising ways for restoring inland eel stocks.