Lakes Shinji and Nakaumi form a coupled brackish lake system on the Japan Sea coast of Japan, and seawater frequently intrudes into these lakes. The study analyzed the influence of river discharge, tide level, and meteorological forcing on seawater flux at Nakaura Watergate. Continuous wavelet transform (CWT), wavelet coherence (WTC), crosswavelet transform (XWT), and partial wavelet coherence (PWC) were used to analyze seawater intrusion. CWT reveals the characteristics of seawater flux, river discharge, tide level, and meteorological forcing. WTC and XWT showed the correlation between forcing variables and seawater flux. PWC analyzed the impact of river discharge, tide level, and meteorological forcing variables on seawater flux after controlling the effect of all other forcing variables. The results showed that tide level has an impact on seawater flux over 0.5-day and 1-day cycle throughout the analysis period, suggesting that astronomical tides play an important role in the salinity intrusion processes. The river discharge characteristics and its influence on seawater flux were clearly revealed especially during high river flows. Sometimes, atmospheric pressure and wind velocity affect tide level, thereby driving salinity transport. The study reveals the power of wavelet analysis in examining nonlinear time series such as salinity intrusion processes.