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Wetland saline water is the enormous problem faced by rural people in Kalimantan, Indonesia. During rainy season, seawater intrudes wetland aquifer and turns water to saline. Application of membrane silica–pectin is eligible to solve this issue. Sadly, this water contains high concentration of organic matter that contributes to declining of membrane performance. Therefore, coagulation pretreatment is explored to enhance membrane filtration performance. The objective of this work is to investigate the optimum condition of coagulation pretreatment to enhance silica–pectin membrane performance for wetland saline water desalination. Sol gel process was employed to fabricate silica–pectin membrane and calcined via rapid thermal processing technique. Desalination was operated by pervaporation at 25–60°C. Maximum removal of organic matter UV254 was obtained at coagulant 30 g L−1 of 83.5% (pH 7). Combination processes between coagulation pretreatment and silica–pectin membranes offered high water flux at 60°C (12.2 kg m−2 h−1). The UV254 rejection of the feed water with coagulation is 43% higher than without applying coagulation pretreatment. Overall, salt rejection for all processes was extremely good (99.9%). Application of coagulation as pretreatment is promising to enhance performance of silica–pectin membrane for wetland water desalination. [ABSTRACT FROM AUTHOR]