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.