The aim of this paper is to study diurnal fluctuations of the water level in streams draining headwaters and to identify the controlling factors. The fieldwork was carried out in the Gryżynka River catchment, western Poland. The water levels of three streams draining into the headwaters via a group of springs were monitored in the years 2011–2014. Changes in the water pressure and water temperature were recorded by automatic sensors – Schlumberger MiniDiver type. Simultaneously, Barodiver type sensors were used to record air temperature and atmospheric pressure, as it was necessary to adjust the data collected by the MiniDivers calculate the water level. The results showed that diurnal fluctuations in water level of the streams ranged from 2 to 4 cm (approximately 10% of total water depth) and were well correlated with the changes in evapotranspiration as well as air temperature. The observed water level fluctuations likely have resulted from processes occurring in the headwaters. Good correlation with atmospheric conditions indicates control by daily variations of the local climate. However, the relationship with water temperature suggests that fluctuations are also caused by changes in the temperature-dependent water viscosity and, consequently, by diurnal changes in the hydraulic conductivity of the hyporheic zone.