The present study reports the potential of carbon (C) storage in traditional agroforestry systems (i.e., a set of age-old agroforestry systems) under waterlogged environmental conditions from north-eastern India. An experiment was conducted in a farmer’s field and further used CO₂FIX model, allometric equations, and destructive sampling methods to know the potential of C sequestration. In this study area, agroforestry system is dominated by woody perennials like Areca catechu, Cocos nucifera, Mangifera indica, Artocarpus heterophyllus, Melocanna baccifera, and Colocasia esculenta as annual crop component. Need-based management of the drainage system has been built-up by making broad/narrow bunds for maintaining water levels at different stages of plant growth. The total annual carbon storage potential of this traditional agroforestry system was estimated as 103.760±8.630 t ha⁻¹year⁻¹. The highest annual carbon storage potential (97.900±8.090 t ha⁻¹year⁻¹) was recorded in annual crop components (i.e., Colocasia) followed by trees and its underlaid soil (4.250±0.340 t ha⁻¹year⁻¹) and lowest for bamboos (1.610± 0. 200 t ha⁻¹ year⁻¹). However, the estimated carbon stored, annually, was 24.992±1.502 t ha⁻¹ year⁻¹ in which Colocasia share maximum contribution (19.600±1.080 t ha⁻¹ year⁻¹) followed by trees + soil (3.798±0.229 t ha⁻¹ year⁻¹) and the minimum contribution from bamboos (1.594±0.193 t ha⁻¹ year⁻¹). Moreover, total carbon loss from harvesting of this system was 78.768±7.128 t ha⁻¹ year⁻¹. The study, therefore, recommends this agroforestry system for other waterlogged ecosystems at regional and/or global scale under a warm per-humid climate for both livelihood opportunities and environmental sustainability.