We investigated the salinity changes of Pulicat lagoon connected to the Bay of Bengal, during the period 1996-2015. Our objective was to drive useful perspectives on the annual, seasonal and sectoral trends of salinity changes using available datasets on salinity, precipitation, and sea-entrance closures. Annual mean salinities randomly correlated with the extent of rainfall. Highest dilution (89-91%) was observed for POE in 1997 and highest concentration in PRE was recorded in 1999 and 2005 (15.2-20.2%) with respect to mean salinity. Predominant changes were evident at the cross-over from dry season ("PRE"; February to September) to wet season ("POE"; October to January). Geostatistical models of PRE and POE salinities provided estimates to be 35.6 ± 4.1 ppt and 25.5 ± 12.9 ppt, respectively. Secondary salinization from runoff contributes to the increase in the salinities in the POE. Sectoral analyses of salinity deviations from mean revealed that the magnitude of desalination due to monsoonal dilution increased with distance from the sea under conditions of exclusivity to riverine influences (e.g. a decrease of~12.41 ppt observed in 2015). Eastern sector experienced highest dilution in POE (100%; year 1997) as well as increase in PRE (22.9%; 1999). Lowest deviations in POE were observed in southern sector in POE (81.5%). The sensitivity of the various sectors to regime shifts from low magnitude salinity change decreases in the order: Western > Southern > Central > Eastern. Our results further emphasize the need for systematic monitoring of salinity distributions to understand ecosystem dynamics at multiple scales.