The Valdivia River estuary (VRE) located in south-central Chile is known as one of the largest estuarine ecosystems on the Pacific coast. This research aims to determine the intra-tidal and sub-tidal variability of saline intrusions into the VRE between November 2017 and March 2019 derived from salinity sensors located along the VRE. Complementary hydrographic measurements were conducted during flood and ebb conditions of the spring and neap tides for each of the four seasons of the year along the central axis of the VRE. The results of the salinity time series showed that saline intrusions (values greater than 0.5 Practical Salinity Units) occurred ~20 km from the estuary mouth, when the total flow of the Cruces and Calle-Calle rivers (main tributaries of the estuary) was low, around 280–300 m3 s−1. During the same period, the best co-variability was observed between the saline intrusions and the mixed-semidiurnal tide and the fortnightly and monthly periods of the tide. Regression analyses indicated that salinity intrusion length (L) is best correlated to discharge (D) with a fractional power model L α D−1/2.64 (R2 = 0.88). The decreasing discharge trend, found between 2008–2019, implies that saline water intrusions would negatively impact the Valdivia’s main drinking water intake during the low rainfall season under future climate conditions.