The abandonment of traditional rural life in mountain areas has favoured the expansion of forest in the headwaters of Pyrenean rivers. In this paper, we (i) analyse hydro-climatic trends at the annual and monthly scales in three nested sub-catchments in a central Pyrenean basin and (ii) quantify the relative contribution of climate change and forest cover on the observed changes in runoff. Land use maps indicate an increase in the forest cover in all sub-basins for the period 1987-2009. Non-parametric Mann-Kendall statistic on annual and monthly hydro-climatic data from 1965 to 2009 was used to identify trends in climate and runoff data. To assess the potential influence of the period length, trends were also examined for the 1941-2009 stretch. Upward trends were detected for temperature and potential evapotranspiration, particularly during summer and winter months. Precipitation trends and their significance depended on the length of the period considered, although overall results indicated a decrease, particularly for February and July. The effects of climate change and land cover change on annual runoff were identified by means of a change point analysis. Results indicated that a change in annual runoff took place in the 1980s, suggesting the non-linearity in the relationship between precipitation and runoff, and thus the influence of land use factors. The influence of forest cover was confirmed by comparing observed runoff trends with those resulting from a hydro-climatic model that does not take into account land use changes. Divergence between both trends revealed that forest cover can account for~40% of the observed decrease in annual runoff.