Watershed and river managers often face difficult choices between safety issues related to floods and degraded hydraulic structures, requiring urgent works and involving environmental stakes such as biodiversity, landscapes and rare species. These choices require taking precise ecological data and existing knowledge into account. Unfortunately, such databases and pre-existing knowledge are rarely available or they are only fragmentary and exist at the local scale for parts of areas classified as protected, or they are limited to a few species. Obtaining these data is time and money consuming and requires significant means, which is incompatible with the need to take urgent decisions. The aim of our work was to develop a flexible, easy to use and rapid method that does not wholly rely on accurate and comprehensive datasets and knowledge. It was designed to meet the need for fast assessment with limited means, which is a frequent case, particularly when urgent decisions are required or when the human and environmental stakes are circumscribable. The method uses an indicator-based approach to assess the effects of various management scenarios on the systems. Actions leading to the potential mitigation of these effects can be proposed. The method was implemented on the Grand Buech river in La Faurie (French Alps) where works were required to improve the safety of dikes. The impact of three management scenarios was assessed on 8 species and habitats. The results showed that, in the medium term, two scenarios may improve the current situation while the last one could worsen it. The method could be adapted to most watersheds and impact assessment in other environments.