While seagrass meadows are perceived to be pertinent blue carbon reservoirs, they also potentially release methane (CH4) into the atmosphere. Seasonal and diurnal variations in CH4 emissions from a subtropical hypersaline lagoon dominated by Halodule wrightii in southern Texas, USA, on the northwest coast of the Gulf of Mexico were investigated. Dissolved CH4 concentrations decreased in the daytime and increased overnight during the diel observation period, which could be explained by photosynthesis and respiration of seagrasses. Photosynthetic oxygen was found to significantly reduce CH4 emissions from seagrass sediment. Diffusive transport contributed slightly to the release of CH4 from the sediment to the water column, while plant mediation might be the primary mechanism. The diffusive CH4 flux at the sea-air interface was 12.3–816.2 µmol/m2 d, over the range of the sea-air fluxes previously reported from other seagrass meadows. This was related to relatively higher dissolved CH4 concentrations (11.6–258.2 nmol/L) in a mostly closed lagoon with restricted water exchange. This study emphasizes seagrass meadows in the subtropical hypersaline lagoon as a source of atmospheric CH4, providing insights into the interactions between seagrass ecosystems and methane dynamics, with potential implications for seagrass meadow management and conservation efforts.