The lower St Johns River is a low-gradient coastal river with tidal hydrodynamics that remain active from the Atlantic Ocean through to the upstream end of Lake George (river km 200). Salinity in the lower St Johns River is spatially and temporally variable, whereby the salinity distribution is driven primarily by the combination of ocean processes of tides and storm surges and hydrological processes of watershed runoff. This study examines the probability distributions and modes of behavior of salinity for present-day conditions using data, numerical modeling and eigen-analysis. The hypothesis is that long-term changes (decadal scale) in the ocean processes will cause the probability distributions of salinity to adjust, and therefore there is a quantifiable non-stationarity of salinity in the lower St Johns River (shifts in the probability distribution of salinity, as representative of salinity increase) due to sea-level rise. The numerical modeling is validated against data, then the model is applied to generate synthetic salinity records for the main river stem and tributaries of the lower St. Johns based on present-day conditions. The synthetic salinity records are transformed into probability distribution functions (PDFs) and eigen-functions. The same analysis is performed on synthetic salinity records generated by the model when applied in forecast mode (i.e., sea-level rise). Comparisons of the forecasted PDFs and eigen-functions with those for present-day conditions quantify the non-stationarity (shifts in probability distributions and changes in eigen-structure) of the salinity in the lower St Johns River. The underlying physics of the cause (sea-level rise)-effect (non-stationarity of salinity) relationship are assessed in terms of coastal/river hydrodynamics