Mangrove ecosystems perform number of important ecological functions and provide a wide range of services at the local or national level and provide a unique combination of both organic matter production and sequestration, which is different from other coastal ecosystems. Mangroves are extensively used to extract twigs and branches for the construction of "Brush piles", the predominant fishing devices in the Negombo estuary, Sri Lanka, believed to have one major impact on the vegetation structure followed by the changes in primary productivity and carbon assimilation capacity of the ecosystem. Present study was conducted with an objective of quantify and relationships between the vegetation structure and Gross Primary Productivity (GPP) of disturbed and natural mangrove stands in the Negombo estuary. Vegetation structural parameters were gathered according to the standard procedures and the measurement of Photosynthetically Active Radiation (PAR) used to calculate the Leaf Area Index (LAI) followed by the GPP. Highest values of vegetation structural parameters, LAI and GPP were recorded from estuarine waterfront and decreased with landwards, which indicated more active vegetation is near by the estuarine waterfront. Comparatively, vegetation structural/structural complexity (CI) and GPP/carbon assimilation capacity were superior in undisturbed/ natural mangrove stands (31.86-36.65