This study evaluates runoff and different methods for the estimation of water balance and runoff genesis in four small alpine catchments, which lie outside the standard network of hydrological and climate networks. These test catchments, whose size ranges between 2.3 and 110 ha, are located above the timberline at elevations between 1,784 and 2,380 m. Their land surfaces consist of lakes, rock formations, debris deposits, and alpine meadows. Hydrological data were collected for the water year 2001. The catchments were instrumented by three automatic weather stations recording global and net solar radiation, air temperature, humidity, precipitation, and soil temperature. Lake water levels were registered with staff gauges and runoff evaluated from water storage calculations. Runoff genesis was investigated by means of chemical tracers (Rhodamine WT and Lithium chloride). Hydrological process estimations were made using standard methods including: the input of precipitation and snowmelt, both potential and actual evaporation, which was estimated by the approaches of Hamon, Priestley-Taylor, Penman and Grindley, and runoff calculated from the lake storage, were compared with results of the conceptual hydrological Brook90 model. The empirical results show that hydrological processes are governed by the temperature-dependent regime of high mountain snowmelt. However, the major differences in water yield and runoff genesis between watersheds were due to differences in the morphologies of the lakes and their basins, the soilvegetation complex, and runoff routing. Evaluating approaches to estimation, Penman’s combination of both aerodynamic and energy balance method provides the best fit to observed data with observed evapotranspiration being 78 to 99% of the potential calculated. The deterministic Brook90 model is effective for precipitation-runoff genesis studies in small headwater catchments. In the L’adové pleso basin predicted and observed water yield show close correlation. The annual sum of actual evapotranspiration calculated by BROOK90 (352 mm) corresponds closely to that estimated by the approach of Penman (386 mm).