Mangrove ecosystems are crucial blue carbon sinks, yet limited studies have quantified greenhouse gas (GHG) fluxes, particularly from sediments, in Indonesia. This study addresses that gap by measuring sediment-based fluxes of carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O) across mangrove zones in Benoa Bay, South Bali during wet and dry seasons. GHG fluxes ranged from 164.7–6529.9 µgmol·m⁻²·h⁻¹ for CO₂, −27.6–166.8 µgmol·m⁻²·h⁻¹ for CH₄, and −4.1–4.4 µgmol·m⁻²·h⁻¹ for N₂O. CO₂ consistently acted as a source, while CH₄ and N₂O fluctuated between sources and sinks, particularly during the wet season. Although no significant seasonal or spatial differences were observed, fluxes were strongly influenced by soil properties (pH, bulk density, total Kjeldahl nitrogen) and porewater characteristics (pH, salinity, redox potential, and dissolved oxygen). These findings highlight the dominant role of sediment and water chemistry in regulating GHG emissions. The study provides essential baseline data for national carbon accounting and underscores the need for integrating sediment management in mangrove restoration. Long-term monitoring is recommended to capture interannual variability and land-use change impacts.