Mangroves play an important role in carbon cycling and are receiving considerable attention to restore degraded areas. Accelerated Natural Regeneration of Mangrove (ANRM) is an approach practiced in Anawilundawa Wetland Ramsar Sanctuary in Sri Lanka since 2019 to restore mangroves in abandoned shrimp ponds. This study was conducted in 2023 to measure the Total Ecosystem Carbon Stocks (TECS) in remnant natural mangroves, areas restored using ANRM, adjacent landward woody areas and abandoned shrimp ponds which are currently covered with secondary vegetation. TECS were 216.98 ± 15.00 Mg C ha− 1 (natural mangroves), 212.58 ± 33.42 Mg C ha− 1 (restored areas), 280.75 ± 30.37 Mg C ha− 1 (woody area) and 348.12 ± 12.83 Mg C ha− 1 (abandoned shrimp ponds). The highest soil organic carbon (SOC) was found in abandoned shrimp ponds (347.48 ± 12.48 Mg C ha− 1) while the lowest SOC was reported in the woody area (170.14 ± 18.09 Mg C ha− 1). The mean total vegetation carbon (aboveground and belowground carbon combined) was the highest in the woody area with 83.51 ± 12.38 Mg C ha− 1. The vegetation carbon stocks of natural mangroves, restored area and abandoned shrimp ponds were 33.67 ± 8.81 Mg C ha− 1, 1.09 ± 0.24 Mg C ha− 1 and 0.64 ± 0.35 Mg C ha− 1 respectively. This study highlighted higher SOC in abandoned shrimp ponds resulting in the highest TECS. They contain the saltmarsh species Suaeda maritima, Suaeda monoica, and Tamarix indica, perhaps highlighting the potential contribution of secondary vegetation in disturbed areas. Changes in elevation, soil composition and residual carbon from aquaculture practices might also influence results, warranting further investigation to understand restoration responses.