The paper presents a modeling framework to analyze the effect of episodic rainfall supply on groundwater dynamics in the Ionian coastal plain multilayered aquifer. The focus is essentially on the short-term behavior of the shallowest layer, with a specific analysis on episodic rainfall events. In the studied aquifer, groundwater level responds sensitively to rainfall events, highlighting the presence of preferential recharge zones. The hydraulic head peak is a function of groundwater level antecedent to the rainfall event. A kinematic dispersion wave model was used to model infiltration processes via preferential pathways. A one-dimensional and non-linear particle based numerical model was developed. Particles with constant water volume travel according to celerity and hydraulic dispersion to simulate the infiltration rate wave through the vadose zone. The flow rate that reaches the water table represents the input function to determine groundwater level fluctuations along groundwater flow direction and according to the lithological features of the surficial levels of the multilayered aquifer, its storage capacity changes passing from unconfined to confined conditions. The model was validated with high time resolution time series of precipitation and groundwater level coming from Terra Montonata meteo-climatic and groundwater level monitoring station. The developed model represents a basis for evaluating and predicting groundwater discharge of the shallowest layers of the Ionian coastal multilayered aquifer under natural conditions including episodic rainfall.