Deep preferential percolation of melt water in snow and firn brings water lower along the vertical profile than a laterally homogeneous wetting front. This widely recognized process is an important source of uncertainty in simulations of subsurface temperature, density, and water content in seasonal snow and in firn packs on glaciers and ice sheets. However, observation and quantification of preferential flow is challenging and therefore it is not accounted for by most of the contemporary snow/firn models. Here we use temperature measurements in the accumulation zone of Lomonosovfonna, Svalbard, done in April 2012–2015 using multiple thermistor strings to describe the process of water percolation in snow and firn. Effects of water flow through the snow and firn profile are further explored using a coupled surface energy balance - firn model forced by the output of the regional climate model WRF. In situ air temperature, radiation, and surface height change measurements are used to constrain the surface energy and mass fluxes. To account for the effects of preferential water flow in snow and firn we test a set of depth-dependent functions allocating a certain fraction of the melt water available at the surface to each snow/firn layer. Experiments are performed for a range of characteristic percolation depths and results indicate a reduction in root mean square difference between the modeled and measured temperature by up to a factor of two compared to the results from the default water infiltration scheme. This illustrates the significance of accounting for preferential water percolation to simulate subsurface conditions. The suggested approach to parameterization of the preferential water flow requires low additional computational cost and can be implemented in layered snow/firn models applied both at local and regional scales, for distributed domains with multiple mesh points.