Globally the number of relatively deep, isolated lakes is increasing because of sand, gravel, or clay excavation activities. The major excavation areas are located within the delta of rivers, and thus the deep freshwater ecosystems formed upon excavation, called quarry lakes, are unique to the landscape. They are embedded in a landscape comprised of shallow, naturally formed lakes. Given that quarry lakes are by definition novel ecosystems, water managers face difficulties in optimally managing them to deliver ecosystem services using existing frameworks designed for natural ecosystems. All lakes in delta areas are subject to similar pressures such as urbanization and eutrophication, leading to shifts in biodiversity and ecosystem functioning, and ultimately changing the ecosystem services the systems can provide. We propose a framework to enable water managers to assess the provision of ecosystem services by quarry lakes based on their ecological quality. For each ecosystem service we determined threshold values of ecological quality based on available scientific literature, an extensive field survey of 51 quarry lakes in the Netherlands, or expert knowledge. To illustrate the usefulness of our approach, we applied our framework to a lake before and after a rehabilitation focused on improving the nutrient status of the waterbody. Assessing ecosystem services under varying levels of ecological health is important to initiate action from legislators, managers, and communities.