•A new method for groundwater recharge estimation in karst is proposed.•A simple conceptual model of soil cover, epikarst and vadose zone is developed.•Partial cross-correlation function is used as objective function.•Applicability of five existing empirical models to the Dinaric karst is analyzed. Aquifers with time variant catchment boundaries, regional flows, and inflows from surface streams and accumulations are common in karst areas. Due to the lack of reliable methods for determination of water balance in the phreatic zone of such aquifers, groundwater recharge estimation is a challenge task. This paper introduces a new method for estimation of groundwater recharge in karst – the so-called partial correlation method (PCM). The basic hypothesis is that the groundwater recharge rates can be determined from the time series of precipitation, air temperature, relative humidity, and spring discharge, by using a partial cross-correlation function as objective function. Following this hypothesis, a simple conceptual model of water balance in the soil cover, epikarst and vadose zone is developed, and an objective function for estimation of the optimal value of parameter of this model is proposed. PCM is applied on the catchment of Žrnovnica Spring located in the Dinaric karst area of Croatia. The results of application are compared with the results of previous studies, as well as with the results obtained by five empirical models that have been used for estimation of groundwater recharge in the Mediterranean karst. The effective infiltration coefficients obtained by PCM for the Žrnovnica Spring are generally in accordance with the previously published ones.