Lagoons are coastal waterbodies which are sensitive to meteorological and hydrological changes. This study focused on the spatial distribution of salinity in Gialova lagoon, Greece. The area in which the lagoon is located is under pressure from agriculture and truism in the area. Besides that, the lagoon is an important stop for migratory birds as well as the home for rare species. To investigate how salinity is distributed in the lagoon a salinity gradient was produced. Also, an attempt was made to model the salt and fresh water fluxes in the lagoon using a mass balance approach. The water fluxes are either from fresh water sources or influx of saline water from the sea. Manual electric conductivity measurements were taken during a field campaign to the lagoon. Time series data used in the model was obtained from stations in the lagoon and the surroundings. An investigation in how the lagoon measurement station differ in salinity was also performed in this study. Results from the gradient map and manual measurements show that the water in the lagoon is the freshest in the North-Eastern parts and the most saline to the South-West. The modelled water fluxes show an inverse relationship from each other. High fresh water fluxes correspond to precipitation events, lower salinity concentration. Whereas high salt water fluxes correspond to high salinity concentration and lowered precipitation. The stations concentrated to the middle lagoon show corresponding values in salinity whereas the station to the South-West differs. The canal surrounding the lagoon shows interactions since measurements show that the water is brackish. A longer time series could provide patterns in water fluxes over time. Trying to find the portions of terrestrial groundwater and surface water, and further investigation of the regional aquifer could provide new information to develop this model. The region is expected to experience water stress which makes further studies and monitoring important.