Seagrasses and mangroves are crucial sources of atmospheric methane (CH₄) from coastal areas. To study the dynamics of CH₄ cycling at subtropical seagrass and mangrove, we studied diurnal CH₄ emissions at the sea-air and sediment-water interfaces and related environmental parameters in August 2019 at lagoonal estuaries of southern Texas, USA, northwest coast of the Gulf of Mexico. Although seagrass meadows and mangroves locate at closely connected subtropical estuaries, they displayed distinct mechanisms in CH₄ cycling. Dissolved CH₄ concentration at the seagrass meadow decreased in the daytime and increased overnight, expressing a tight relationship with photosynthesis and respiration of seagrass. Plant mediation of seagrass played a crucial role in CH₄ production, oxidation, and transport from sediment to water column. In comparison, the diel variation of dissolved CH₄ concentration at the mangrove creek was controlled by tidal progression. The maximum CH₄ level occurred during ebb due to the export of CH₄ from inside the mangrove to the outside bay. Tidal pumping and tidal inundation were essential conduits for dissolved CH₄ exchange between water and porewater. In both areas, sea-air CH₄ fluxes were significantly affected by wind speeds, which hid related diurnal variations caused by physiological or tidal cycles. Our study also revealed a more significant contribution from seagrass to the local CH₄ budget than from mangroves, indicating CH₄ released from subtropical seagrass needs further investigation.