Hydrological droughts are expected to increase in frequency and severity due to changing climate in several river basins. Recent severe droughts, like the 2018 drought in northwestern Europe, have shown major challenges for water management, not only in terms of water quantity, but also water quality. However, these water quality impacts have received far less attention, and limited understanding exists, in particular regarding concentration responses of emerging chemicals, such as pharmaceutical in surface waters under droughts. This study therefore shows the impacts of the 2018 drought on the water quality of the Rhine and Meuse rivers (Western Europe) focusing on a selection of water quality parameters relevant to multiple sectoral water uses and ecosystem health, i.e. water temperature, salinity and four pharmaceuticals (carbamazepine, metoprolol, ibuprofen and sulfamethoxazole). Surface water quality data of six monitoring stations (mainly in the Netherlands) were analyzed for the 2018 drought in comparison to the reference period 2014–2017. Our results show that low flow combined with high temperatures resulted in a general deterioration of surface water quality of both the Meuse and Rhine rivers during the 2018 drought. This was reflected by significant increases in water temperatures (average of +1.9 °C) and salinity levels (+11%). While we found higher concentrations of some pharmaceuticals (carbamazepine (+10%) and metoprolol (+29%)), these increases were statistically insignificant. The decline in water quality is primarily caused by limited dilution of the chemical load derived from point sources and salinity intrusion in the lower part of Rhine-Meuse delta. A comparison of the water quality responses of the Rhine and Meuse shows larger impacts for the rainfed Meuse river with lower summer flow, compared to the mixed rain- and snowmelt-fed Rhine river. Sustainable, transboundary river water management is essential to ensure water of suitable quality for different sectoral uses during future projected droughts.