This study was carried out to determine the distribution and variability of soil salinity at the recently irrigated margins of the Akyatan lagoon and saline wetlands located in the Lower Seyhan basin in Adana, the eastern Mediterranean region of Turkey. An EM38-DD field apparatus was used to measure the apparent electrical conductivity of the soil expressed as ECv in order to shed light on the spatial variability of salinity of the area by monthly observations conducted at 50 points. The salinity measurements were conducted from June 2005 to November 2006, and in July and November 2018, and in March 2019. The ECv values decreased with distance from the lagoon and the wetlands towards the upper and/or central parts of the basin. A comparison of the distributions of salinity showed that salt-affected soils corresponded to the high electrical conductivity of the water-table. The changes in soil salinity indicated that salinization was the result of capillary rise and evaporation from the saline shallow water-table. The electrical conductivity of several soil series and varying land management revealed that the ECv values above 200 mS/m significantly hinder plant growth, however, land use practices (i.e., crop rotation) slightly affected the fluctuation level of salinization. The ECv values of the rainy seasons were generally lower than those of the dry periods. It can be concluded that the topographic position (e.g., distance to the lagoon), soil texture, and the saline shallow water-table along with the inappropriate soil and micro-topographic conditions, are the most effective factors for salinity build up.