Water resources and aquatic ecosystems are an essential concern of any policy for sustainable development. In the context of the European Water Framework Directive, which aims to achieve good chemical and ecological status of waters, the herbicide diuron was banned in France in December 2008. In lotic ecosystems, benthic microbial assemblages are considered as useful potential indicators of ecological status because they integrate the effects of multiple anthropogenic disturbances and have strong capacities to adapt to novel environmental conditions. Field studies have thus revealed that in situ diuron exposure can induce microbial adaptation leading to an increase in diuron biodegradation potential of sediment microbial communities. It suggests that microbial biodegradation capacities can represent a powerful ecological indicator for monitoring spatio-temporal variations in pesticide contamination and evaluating associated ecological effects. The aim of this study was thus to evaluate the use of freshwater sediment biodegradation potential as an ecological indicator for monitoring microbial recovery following a decrease in chronic pesticide exposure. For this purpose, a four-year case study (2008–2011) was conducted in a small stream (Morcille river) long exposed to high diuron concentrations, increasing from upstream to downstream. Our results show that the ban on diuron resulted in a progressive decrease in its concentrations in the Morcille river over the survey period. The decrease in the level of chronic diuron exposure in the river caused a fall in sediment diuron-mineralizing capacities, assessed by radiorespirometry using [ring-U-14C] diuron. It thus revealed a corresponding recovery of microbial communities, showing that the use of freshwater sediment biodegradation potential may be useful for assessing microbial recovery after a decrease in chronic exposure to pollutants, opening prospects for developing a new class of ecological indicator to monitor the recovery of biological quality of water resources.