The estimation of groundwater recharge is of paramount importance to assess the sustainability of groundwater use in aquifers around the world. Estimation of the recharge flux, however, remains notoriously difficult. In this study the application of nonlinear transfer function noise (TFN) models using impulse response functions is explored to simulate groundwater levels and estimate groundwater recharge. A nonlinear root zone model that simulates recharge is developed and implemented in a TFN model and is compared to a more commonly used linear recharge model. An additional novel aspect of this study is the use of an autoregressive-moving-average noise model so that the remaining noise fulfills the statistical conditions to reliably estimate parameter uncertainties and compute the confidence intervals of the recharge estimates. The models are calibrated on groundwater-level data observed at the Wagna hydrological research station in the southeastern part of Austria. The nonlinear model improves the simulation of groundwater levels compared to the linear model. The annual recharge rates estimated with the nonlinear model are comparable to the average seepage rates observed with two lysimeters. The recharges estimates from the nonlinear model are also in reasonably good agreement with the lysimeter data at the smaller timescale of recharge per 10 d. This is an improvement over previous studies that used comparable methods but only reported annual recharge rates. The presented framework requires limited input data (precipitation, potential evaporation, and groundwater levels) and can easily be extended to support applications in different hydrogeological settings than those presented here.