Wetland water is an alternative water resource around wetland areas. However, it is typically saline due to seawater intrusion and contains high natural organic matter (NOM) that is challenging to treat. This study evaluated the stability of interlayer-free mesoporous silica matrix membranes employing a dual acid–base catalyzed sol–gel process for treatment of saline wetland water. The silica sols were prepared under a low silanol concentration, dip-coated in 4 layers, and calcined using the rapid thermal processing method. The membrane performance was initially evaluated through pervaporation under various temperatures (25–60 °C) using various feeds. Next, the long-term stability (up to 400 h) of wetland saline water desalination was evaluated. Results show that the water flux increased at higher temperatures up to 6.9 and 6.5 kg·m−2·h−1 at the highest temperature of 60 °C for the seawater and the wetland saline water feeds, respectively. The long-term stability demonstrated a stable performance without flux and rejection decline up to 170 h operation, beyond which slow declines in water flux and rejection were observed due to fouling by NOM and membrane wetting. The overall findings suggest that an interlayer-free mesoporous silica membrane offers excellent performance and high salt rejection (80–99%) for wetland saline water treatments.