In this paper, we present an approach based on the simultaneous use of multilevel monitoring systems for the ground and surface water and wavelet-based analysis of the time series observed to detect the main mechanisms influencing the water level, electrical conductivity (EC) and temperature (T) in ground and surface water of the river Neretva coastal aquifer system. Although the area of interest is under significant impact of seawater intrusion, the presented approach enabled the insight to transient response of the system to external loadings like precipitation and irrigation system primarily. The capacity of the monitoring system has been demonstrated on two different subareas, respectively, Diga and Jasenska. While the Diga area is shown to be under significant influence of the seawater, the Jasenska area shows sensitivity to precipitation and pumping station (PS) Modric operative regime. Groundwater parameters as observed during dry periods at Jasenska show the presence of stratification. Wavelet-based analysis enabled the determination of the interdependence of the variables of interest as well as their temporal dependence. Determined regimes of the surface water, as found within the Jasenska channel, are additionally supported by the in situ profiling results, thus strengthening the findings of the study. Our findings reflect the capacity of the approach to capture for the stratification of the groundwater parameters induced by seawater intrusion and external loadings.