Intense sand and gravel mining has created numerous man-made lakes around the world in the past century. These small quarry lakes (1–50 ha) are usually hydrologically isolated, often deep (6–40 m) and stratify during summer and in cold winters. Due to their small size, these deep man-made lakes are usually not included in the regular monitoring campaigns, e.g. as required for the European Water Framework Directive (WFD). Therefore, not much is known about the ecological functioning of these novel ecosystems. During two summers, we determined the macrophyte diversity and measured a range of physico-chemical and biological parameters in 51 quarry lakes in the catchment area of the rivers Meuse and Rhine. We compared the results of this campaign to the chemical and macrophyte sampling as performed for the WFD in the immediate surrounding shallow standing waters. Alpha (local) and beta diversity (regional), and local contribution to beta diversity were calculated for the whole region of which beta diversity was further partitioned into a true species replacement and richness difference component. Quarry lakes contain higher water quality reflected by lower nutrient and chlorophyll-a concentration compared with shallow water bodies. Additionally, quarry lakes contribute significantly to the regional macrophyte diversity pool by harboring distinctly different macrophyte communities (beta diversity — replacement). Specifically quarry lakes with a total phosphorus concentration in the water column below 35 μg P/l contribute most to beta diversity among quarry lakes. Novel ecosystems such as deep quarry lakes are often perceived as less valuable ecosystems, with strong implications regarding their management. Our results show that quarry lakes are in general of better chemical and biological quality compared with shallow standing waters. We therefore call for a more integrated assessment of the quality of quarry lakes and corresponding management strategy of these waters by water managers.