A state-space model (SSM) of infiltration estimates daily groundwater recharge using time-series of groundwater-level altitude and meteorological inputs (liquid precipitation, snowmelt, and evapotranspiration). The model includes diffuse and preferential flow through the unsaturated zone, where preferential flow is a function of liquid precipitation and snowmelt rates and a threshold rate, above which there is direct recharge to the water table. Model parameters are estimated over seasonal periods and the SSM is coupled with the Kalman Filter (KF) to assimilate recent observations (hydraulic head) and meteorological inputs into recharge estimates. The approach can take advantage of real-time hydrologic and meteorological data to deliver real-time recharge estimates. The model is demonstrated on daily observations from two bedrock wells in carbonate aquifers of northwestern New York (USA) between 2013 and 2018. Meteorological inputs for liquid precipitation and snowmelt are compiled from SNODAS (2021). Results for recharge during winter and spring seasons show preferential flow events to the water table from liquid precipitation, snowmelt, or a combination of the two. Recharge estimates summed annually are consistent with previous estimates of recharge reported from groundwater flow and surface-process models. Results from the SSM and KF point to errors in meteorological inputs, such as the snowmelt rate, that are not compatible with hydraulic head observations. Whereas liquid and solid precipitation are measured at discrete stations and extrapolated to 1-km² grid cells, snowmelt is a meteorological modeled outcome that may not represent conditions in the vicinity of monitoring well locations.