This study provides the first integrated assessment of diel, seasonal, and annual methane (CH₄) dynamics in Taiwan’s seagrass ecosystems, focusing on the Haikou seagrass meadow and adjacent coastal waters. From May 2022 to June 2023, field campaigns combined surface water sampling, in situ benthic chamber incubations and porewater profiling in both seagrass and bare sand habitats to evaluate CH₄ fluxes at the sediment–water and water–air interfaces. Results showed similar temperature and salinity patterns between seagrass and coastal waters, but seagrass habitats exhibited strong diurnal oxygen fluctuations that suppressed daytime CH₄ accumulation. Seagrass habitats consistently had higher CH₄ concentrations and sea-to-air fluxes than other coastal area, with nighttime emissions exceeding daytime values and autumn fluxes peaking under windy conditions. Sediment incubations identified benthic processes as the dominant CH₄ source. Seagrass sediments sustained relatively stable fluxes across seasons, while sandy sediment produced episodic pulses during storm events. Porewater profiles revealed elevated CH₄ in the upper 12 cm of sediments, especially in seagrass, with declines at depth due to substrate limitation and anaerobic oxidation. At the ecosystem scale, the Haikou seagrass meadow emitted approximately 78.3 mol CH₄ yr⁻¹ to the atmosphere from the water column, while sediments released 1,410.1 mol CH₄ yr⁻¹ into the water column, 94 % of which was oxidized before reaching the atmosphere or transported laterally. These fluxes are ecologically significant, emphasizing the dual role of seagrass meadows as carbon sinks and localized sources of CH₄ within tropical coastal ecosystems in Taiwan.