Lake Shinji and Lake Nakaumi are coupled brackish lakes on the Japan Sea coast of Japan. Seawater from the Japan Sea frequently intrudes into Lake Nakaumi through the bottom. Salinity flux at Nakaura Watergate was analysed. Effects of river discharge, tide level, and meteorological forcing variables makes the seawater intrusion non-linear. To account for the non-linear characteristics, partial wavelet coherence (PWC) was used to analyse the impact of river discharge, tide level, and meteorological forcing variables on salinity flux after controlling the effect of all other forcing variables. PWC results show that tide level has impact on salinity flux over short cycles (limited to less than 4 days) throughout the analysis period with an average time lag of about 2 days. This suggests that astronomical tides are the dominant factor in the salinity intrusion processes. The river discharge largely influences salinity flux over medium cycles (5-16 days) during the months of June and July with an average time lag of 0.3 days. Atmospheric pressure occasional affect tide level, indirectly driving salinity transport. The study findings provide guidance for factors affecting salinity intrusion processes and further research.