The applied research programme (2015-2020), entitled “Nature Ambitions for the Dutch rivers, lakes and es-tuaries” (Acronym: BO-NAGW) investigated which eco-system conditions are essential for the recovery of nat-ural dynamics in the rivers, lakes and estuaries in the Netherlands in synergy with economic use and exist-ing Natura 2000 objectives. This article describes what we have learnt from the conducted research. Almost at the same time (2017) a programmatic approach, entitled PAGW, was developed by the government in which na-ture development projects are selected and implement-ed to bring these ambitions into practice, The results il-lustrate that food availability and habitat quality are at least as important as extra habitat in order to achieve Natura 2000 objectives. The first choices for addition-al measures to increase the ecological resilience of the water systems have been made (2019). As a result, policy makers formulate more knowledge questions about the cost-effectiveness of nature development measures. We recommend that both research and water management should evaluate ecosystem functioning and the impact of interventions not only at water system level but also at landscape level, considering regional community needs.