In this study, the temporal variation in soil salinity dynamics was monitored and analyzed using Electromagnetic Induction (EMI) in an agricultural area in Port Said, Egypt, which is at risk of soil salinization. To assess soil salinity, repeated CMD2 soil apparent electrical conductivity (ECa) measurements were taken and inverted to generate electromagnetic conductivity imaging (EMCI), representing soil electrical conductivity (σ) distribution through time-lapse inversion. This process involved converting EMCI data into salinity cross sections using a site-specific calibration equation that correlates σ with the electrical conductivity of saturated soil paste extract (ECe) for the collected soil samples. The study was performed from August 2021 to April 2023, involving six surveys during two agriculture seasons. The results demonstrated the accurate prediction ability of soil salinity with R2 value of 0.81. The soil salinity cross sections generated on different dates observed changes in the soil salinity distribution. These changes can be attributed to shifts in irrigation water salinity resulting from canal lining, winter rainfall events, and variations in groundwater salinity. This approach is effective for evaluating agricultural management strategies in irrigated areas where it is necessary to continuously track soil salinity to avoid soil fertility degradation and a decrease in agricultural production and farmer’s income.