Abstract: Background: Setiu wetlands is located in the state of Terengganu facing the Southern part of South China Sea, Malaysia. This wetland has a diverse ecosystem that represents a vast array of biological diversity and abundance in utilizing natural resources. However, there is large scale of aquaculture activities within and nearby the wetland which could threaten the ecosystems of this area. The surface water are the most exposed to pollution due to their easy accessibility to the disposal of wastewaters. Objective: Thus, the main objectives of the study are to determine the surface water distribution of ammonia and phosphorus due to aquaculture activities with respect to the baseline data of these parameters. Methodology: The samples were taken on October, 2014 (dry season) and November, 2014 (wet season) at 18 different areas. It was observed that the impact of human activities such as agriculture and aquaculture were the responsible factors for higher ammonia and phosphorus concentrations recorded in the study area. Results: From the observed results, wet season has high concentration of nutrient where the total ammonia nitrogen during the low tide was (1.5311±0.0419 mg L–1) and during high tide was (1.4298±0.0334 mg L–1). Meanwhile the ortho-phosphate level during the low tide and high tide were (0.0280±0.0048 mg L–1) and (0.0340±0.0230 mg L–1), respectively. Conclusion: Tidal hydrodynamics influenced the changes of the concentration parameters in the water column. More important, the concentration of ammonia and phosphorus in water can determined to monitor the maximum carrying capacity of the aquaculture activities that would not jeopardize a sustainability of ecosystem according to NWQS standard.