Lakes are excellent indicators of environmental health, accumulating pollutants and nutrients from their surroundings. It is moreover imperative to preserve and restore these ecosystems, which face numerous stressors, to mitigate biodiversity loss and maintain their functionality which are essential for the neighbouring populations. In France, restoration efforts predominantly target aquatic hydromorphological components, focusing on reinstating water level fluctuations, re-establishing reedbeds and creating or rehabilitating islands within lakes. Conventional biodiversity monitoring methods are applied to measure the potential positive impact of restoration. These methods, which rely on morphological identification of algae, benthic macrofauna, ichthyofauna and macrophytes, are labor-intensive, need to have access to taxonomic experts, and can be invasive (capture of individual with nets). Consequently, there has been a growing interest in molecular identification techniques such as DNA metabarcoding, enabling rapid and cost-effective assessment of community taxonomic composition and revealing cryptic species, thereby enhancing the resolution of ecosystem assessments. Environmental DNA (eDNA), targeting DNA extracted from environmental samples, provides a comprehensive snapshot of biodiversity within aquatic environments. Lake Geneva (France/Switzerland), the largest lake in Western Europe, suffers from an extreme simplification of its shoreline, which has been almost completely rectified. To reverse this trend, some area were renatured in 2015 with the creation of reed beds, small islands and underwater dykes in compensation of the construction of a harbour in Geneva. Our study aims to elucidate the impacts of the different restoration interventions (namely, breakwater construction, reedbed establishment and vegetation enhancement) on freshwater biodiversity of Lake Geneva's shoreline. We hypothesised that restoration would have a positive impact on alpha and beta diversity and on the stability of ecological networks. Every month for a year, we monitored changes in the benthic and planktonic communities of restored and non-restored shorelines. We sampled environmental DNA in water and in biofilms , targeting three biological compartments which are crucial to ecosystem functioning (algae, macroinvertebrates and fish). We conducted comparisons between restored and non-restored areas and analysed the seasonal changes along the year considering various biological metrics (from diversities to ecological networks analyses) to bring valuable insights into the efficacy of restoration strategies in fostering ecosystem resilience and sustaining biodiversity in freshwater ecosystems.