Water and energy fluxes at and between the land surface, the subsurface and the atmosphere are inextricably linked over all spatio-temporal scales. Our research focuses on the joint analysis of both water and energy fluxes in a pre-alpine catchment (55 km2) in southern Germany, which is part of the Terrestrial Environmental Observatories (TERENO). We use a novel three-dimensional, physically based and distributed modelling approach to reproduce both observed streamflow as an integral measure for water fluxes and heat flux and soil temperature measurements at an observation location over a period of 2 years. While heat fluxes are often used for comparison of the simulations of one-dimensional land surface models, they are rarely used for additional validation of physically based and distributed hydrological modelling approaches. The spatio-temporal variability of the water and energy balance components and their partitioning for dominant land use types of the study region are investigated. The model shows good performance for simulating daily streamflow (Nash–Sutcliffe efficiency > 0.75). Albeit only streamflow measurements are used for calibration, the simulations of hourly heat fluxes and soil temperatures at the observation site also show a good performance, particularly during summer. A limitation of the model is the simulation of temperature-driven heat fluxes during winter, when the soil is covered by snow. An analysis of the simulated spatial fields reveals heat flux patterns that reflect the distribution of the land use and soil types of the catchment. The water and energy partitioning is characterized by a strong seasonal cycle and shows clear differences between the selected land use types. Copyright © 2016 The Authors Hydrological Processes Published by John Wiley & Sons Ltd.