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River discharge, precipitation, wind, water level and salinity measurements were used to investigate saltwater intrusion in a subtropical estuary. The upstream limit of saltwater intrusion was defined by the position of the 2 g/kg isohaline (X-2) as it changed each tidal cycle. Observations were obtained from November 2014 to November 2015 along the Suwannee River, at Florida's Big Bend. Observations provided information to construct a first-order autoregressive Markov-chain model and predict X-2. The model predicts from its position in the previous tidal cycle, from river discharge, from water level, from precipitation and from wind velocity. In order to capture the seasonality of the Suwannee River discharge, the analysis was done separately for high and low river discharge regimes. The high discharge regime for the particular year of observations coincided with the cold season and had a mean value of 360 m(3)/s. The low discharge regime overlapped with the warm season and had a mean of 198 m(3)/s. As expected, saltwater intrusion was inversely related to river discharge. Values of X-2 were 0.4 km for a discharge of 377 m(3)/s, and 6 km for a discharge of 195 m(3)/s. The autoregressive model was able to reproduce the observed seasonality of saltwater intrusion in the Suwannee River. The model was then used to project values of X-2 for different scenarios of climate change as represented by possible combinations of river discharge and water levels.