The first results of the application of the integrated multidisciplinary protocol to study the effects of water level management on the Lake Maggiore littoral habitats and biocoenosis are presented. The "Parchi Verbano Ticino" project (2019-2021, ID: 481668) was the driving force to fine-tune the monitoring and management system of multidisciplinary information (chemistry, hydro-morphology, macro- and meio-fauna monitoring). The study reveals that water level fluctuations in Lake Maggiore, sometimes characterized by measurable changes in water levels, have remarkable effects on littoral habitats and on the structure and function of macro- and meiofaunal assemblages living there. Overall, this study provides insights into the potential impacts of Lake Maggiore water management strategy on freshwater littoral ecosystems during late spring-early summer, and emphasizes the need for a comprehensive understanding of the lake ecosystem dynamics. Thanks to the results achieved, publicly endorsed water management rules will be stated, for the late spring-early summer period, considering frequency and amplitude of water level fluctuations as crucial factors in management plans to mitigate their impacts. The endorsed rules turn out to be a negotiated compromise between the maintenance of ecosystem services and the protection of littoral life below water.