The study aims to address the long‐term impacts of six different downscaled Regional Climate Models (RCM) climate models on the quantity (river flow) and quality (sediment load, total nitrogen load and total phosphorus load) state of surface waters in the river Reka catchment, in the northern Mediterranean. Mediterranean areas are – due to high population density, favourable natural conditions for agriculture, limited water resources, diverse ecosystems biodiversity and expected climate change impacts – a global hotspot in climate research. Additionally, the study area lies on the border with the alpine climate zone, with a strong orographic effect on weather patterns. The location, and a wide range of studied parameters, provides an interesting insight into how various emerging climate change models may impact the status of surface waters and procedures for the governance of water resources. The study contributes to the knowledge and understanding of the climate change impact on the local catchment level, using the ensemble of the RCMs. It opens discussion about the impact of RCM selection on modelling climate changes with catchment models like Soil and Water Assessment Tool. This article also questions the usability of the results for the policy and decision makers in relation to the implementation of the results into short or long‐term water strategies or water/river management plans. Copyright © 2015 John Wiley & Sons, Ltd.