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Groundwater is one of the main sources of water for irrigation used worldwide. However, the application of the resource is threatened by the possibility of high saline levels, especially in low-lying coastal regions. Furthermore, the lack of readily accessible materials for successful treatment procedures makes the purification of such water a constant challenge. Based on the fact that natural zeolite is one of the easily accessible and relatively cheap filter materials, this study examined the potential use of high-salinity groundwater filtered by natural zeolite for irrigation. Zeolite-filled filters at two different depths (0.5 m and 1 m) were studied. The samples were collected from the low-lying areas of Dar es Salaam City, Tanzania. The study observed that when the raw groundwater samples were exposed to the 0.5 m column depth, sodium (Na+) had the lowest removal efficiency at 40.2% and calcium (Ca2+) had the highest removal efficiency at 98.9%. On the other hand, magnesium (Mg2+) had the lowest removal efficiency, at about 61.2%, whereas potassium (K+) had up to about 99.7% removal efficiency from the 1 m column depth treatment system. Additionally, from the salinity hazard potential analysis, most of the samples fell within C4 (based on the electrical conductivity), which is a “very high salinity” class, and based on the quality it means the water cannot be directly applied for irrigation purposes. From the 0.5 m column depth, most of the samples fell within C3 (the “high salinity” class), and from the 1 m column depth most of the samples fell within C1 (“low salinity” class). The findings of this study offer some valuable insight into the prospective use of natural zeolite for the filtration of saline groundwater before its application for irrigation.