Climate change and associated rising in sea water level have affected the salinity in many rivers around the world. It has an effect on the embouchure adjacent with the sea, which is called the salinity intrusion problem. This study investigated the effects of climate change on sea water level that affects the hydraulic conditions, salinity, water supply and agricultural areas in the lower Chao Phraya River by MIKE 11 model has been used. The study covered the area from Chao Phraya Dam (barrage), Chai Nat Province to the river estuary, Samut Prakan Province. The model was divided into two parts, hydrodynamic module and advection-dispersion model. Calibration of each part was done by adjusting its important coefficients. It was observed that the Manning’s coefficient (n) and coefficient dispersion of mass were in the range of 0.025 - 0.40 and 800 - 1600 m2/s, respectively. The results of comparison between models and observation data revealed order of forecasting error (R2) with the range of 0.76-0.99 for water level and 0.73 - 0.86 for salinity. The RCP 8.5 scenario from IPCC report was simulated. It was found that sea water level rising in was 1.16 m in the year of 2100, and salinity at SamlaePump Station was risen to 0.37 - 0.75 g/l. The value of 0.25 g/l exceeding standard and the pointed tip of salinity was at Koh Rain District, Ayutthaya Province (137 km from Chao Phraya Dam: CPD). For agricultural sectors, the value of 0.20 g/l exceeding standard and the pointed tip of salinity was at Ban Mai District, Ayutthaya Province (123 km from CPD). Results obtained from this study will give the guideline in raw water resources management for water supply and agricultural in Chao Phraya River Basin.