This study investigates the spatial and seasonal variations in greenhouse gas (GHG) emissions, specifically CO₂ and CH₄, from the Kenyir hydropower reservoir and the downstream Terengganu River system in Malaysia. Elevated GHG concentrations were found near dam discharge outlets, extending up to 12 km along the river, with sand extraction contributing over 50% of the total GHG flux. The estuary exhibited seasonal variations, showing higher CO₂ emissions during the dry season and increased CH₄ emissions in the wet season, further intensified by a breakwater that altered water column mixing and trapped organic-rich runoff. Annually, the Terengganu River catchment emits approximately 565 Gg of CO₂-equivalent, of which 94% originates from the Kenyir Reservoir. Despite its smaller size, the estuary disproportionately contributes to emissions, accounting for 5.5% of the total, due to high organic matter content and reduced water turnover, particularly in the wet season. This study highlights the significant impact of human intervention on the river mouth, which potentially influences GHG dynamics in tropical river-estuary systems and underscores the need for further research in this area.