The aims of this study are: i) to better understand the coupled interactions between land use changes, climate change and the aquatic ecosystem in a small agricultural catchment (<100 km<jats:sup>2</jats:sup>) with a long observation history (1963–2018) and a known land use history, and ii) to test available approaches to separate land use and climate change impacts on water resources in such a small catchment. The pre- and post-change periods have been separated based on change points and the known land use history. Next, conceptual and analytical approaches were applied to quantify and to distinguish between the impacts of climate and land use changes on annual runoff for these two periods. Over the observation period, both land use changes (increase in forest areas) as well as climate change (a temperature rise and a decrease in annual precipitation) occurred. These changes contributed to a decrease in the average annual runoff by 51.9 mm (49% of the long-term average) during the observation period. The quantified contributions of climate and land use changes to the decrease in the mean annual runoff amount to between 60% and 80% and between 40% and 20%, respectively. (i) The results obtained from different methods were consistent - a change in runoff was primarily caused by shifts in climatic variables. (ii) However, the quantified contributions varied depending on the method applied and the form of the Budyko curve. (iii) Thus, special care should be taken in relation to the selection of the Budyko curve for quantifying these changes. (iv) Knowledge of the water deficit sources can result in better planning of water resources management in such small catchments.