Uthokvibhajaprasid Gate was built under the royal patronized projects to develop the agricultural areas in Pakpanang River basin. This was to prevent intrusion of seawater into the agricultural areas of the Pakpanang River basin. The gate located in Tumbol Hulon, Amphur Pakpanang, Nakhon Si Thammarat Province in the southern part of Thailand. The gate started operating in 1999, comprised of 10 sluice gates with a total maximum discharge capacity of 1,430 cubic meters per second. The main objective of this study was to investigate the effects of gate operation on the community structure of the fishery resources in the Pakpanang River and the Pakpanang Bay. The focused areas were in the distances of 46.8 kilometers above and 22.3 kilometers under the gate. The methods used including measuring of salinity distribution, salinity tolerances of the key species, and collecting of fish samples using the small-scale fishing gears. It was found that closing of the gate resulted in changing of aquatic ecosystems in Pakpanang River from partial brackish water at the mouth of the river into whole freshwater ecosystem. This change reduced fish species of the river. Closing of the gate also obstructed flow of the river that reduced spawn-triggering conditions of the freshwater fish. Salinity in Pakpanang Bay increased significantly especially in the spring tides when freshwater discharge was impeded. This results in migration of some economically important marine species into the bay. However, brackish water ecosystem still existed in some certain parts the bay. The gate was to open only to regulate the excess water or to prevent flooding in the rainy season. Opening of the gate in the rainy season resulted in significant dilution of the salinity in the bay. Low salinity conditions together with enrichment of the nutrients contained in the discharged water promoted growth of phytoplankton and fish larvae in the bay. However, change of salinity levels found in this study did not cause migration of fish out of the bay, as the fish species in the bay were mostly euryhaline type. This study also proposed the courses of action taking in how to operate the gate effectively and how to enhance the fishery resources both in the river and the bay.