One of the actions that has been implemented to support the recovery of the panmictic population of European eel is stocking of waterbodies where natural recruitment is low or null. However, growth conditions of the stocked eels can vary greatly. This circumstance emphasises the importance to determine ideal habitat conditions to contribute to the success of stocking actions and, consequently, to increase the production of silver eels. This study aims to evaluate the early settlement and growth of stocked glass eels in the upper reaches of a fragmented river. Stocking was carried out, in 2014, at three sites of an inland tributary of the Mondego river basin (Central Portugal), and its monitoring was conducted during the following two years, until 2016, along with the collection of environmental and hydromorphological parameters. The results showed a successful dispersion throughout the study area. Growth varied spatially, although environmental parameters have not clearly explained this variation, but overall with high growth rates and a positive allometric growth in this early stage of stocking, suggesting a good condition of the stocked individuals. This study showed that these upper reaches of fragmented watercourses, a shared feature amongst most European rivers that are currently inaccessible for natural recruitment, may be suitable habitats for eel stocking.