Saltwater intrusion (SWI) exposed the significant risk to rice production in the tropical lowland delta, especially under the contact of climate change. This study have developed the economic loss functions for both direct and indirect losses caused by SWI after investigating several regression models (such as: Ordinary Least Squares (OLS), Fixed Effects Model (FEM), Random Effects Model (REM), and Feasible Generalized Least Squares (FGLS), based on the 85 questionaires colleted in the tropical rice fields located in Ho Chi Minh City (HCMC). Direct damages were estimated based on cultivated area, rice yield, and salinity levels; while indirect damages were included the costs of water pumping, soil improvement, and irrigation infrastructure construction. The results showed that rice yield decreases sharply when salinity exceeds the threshold level of 1.5 parts per thousand, and indirect costs account for 9% of total damages. The new finding of this study is integrating indirect factors (water pumping, soil improvement, and irrigation infrastructure construction) into the economic loss function, enabling the estimation of both direct and indirect damages cause by SWI; which is a critical tool for water related disasters prevention and management, or land use planning, or developing socio-economic strategies to ensure food security for the deltas strongly affected by SWI.