Understanding how orogenic topography controls the spatial distribution and isotopic composition of precipitation is critical for paleoaltitudinal reconstructions. Here, we determine the isotopic composition (O and δD) of 82 small rivers and springs from small catchments in the Pyrenees. Calculation of the deuterium excess (d-excess) parameter allows the distinction of four distinct isotopic provinces with d-excess values of between 15 and 22‰ in the northwest, between 7 and 14‰ in the central northern Pyrenees and between 3 and 11‰ in the northeast. The southern Pyrenees have a homogenous d-excess signature ranging from 7 to 14‰. Our results show significant local moisture recycling and/or rain amount effect in the northwestern Pyrenees, and control by evaporation processes during rainfall events in the southern Pyrenees and for low elevated samples of the northeast of the range. Based on the distribution of d-excess values, we estimate contrasting isotope lapse rates of −2.9/−21.4‰/km (O/δD) in the northwest, −2.7/−21.4‰/km (O/δD) in the north central and −3.7/−31.7‰/km (O/δD) in the northeastern Pyrenees. The southern Pyrenees show distinctly higher lapse rates of −9.5/−77.5‰/km (O/δD), indicating that in this area the altitudinal effect in not the only parameter driving isotopic composition of rivers. Despite their relatively low topographic gradient, the Pyrenees exert a direct control on the isotopic composition of river waters, especially on their northern side. The variations in isotopic composition–elevation relationships documented along the strike of the range are interpreted to reflect an increasing continentality effect driven by wind trajectories parallel to the range, and mixing with Mediterranean air masses. Despite these effects, the measurable orographic effect on precipitation in the Pyrenees proves that the isotopic composition approach for reconstructing past topography is applicable to low-elevation orogens.