Coastal wetlands are terrestrial-marine transition zones harboring diverse active microbial communities. The origins of diverse glycerol ether lipids preserved in coastal wetlands are rarely investigated. 16 surface sediments were collected from the coastal wetland at Guangrao (GR), Changyi (CY) and Xiamen (XM), where both climate and sedimentary environment show significant differences. Ten groups of glycerol ether lipids, including isoprenoidal and branched glycerol dialkyl glycerol tetraethers (iGDGTs and bGDGTs), isoprenoidal and branched glycerol dialkanol diethers (iGDDs and bGDDs), hydroxylated isoprenoidal GDGTs and GDDs (OH-GDGTs and OH-GDDs), overly branched GDGTs (OB-GDGTs), sparsely branched GDGTs (SB-GDGTs), hybrid isoprenoid/branched GDGTs (IB-GDGTs) and a tentatively assigned H-shaped branched GDGTs (H-B-GDGTs) were detected and quantified. Sediments collected in the north (Guangrao and Changyi) contain, in general, a lower abundance of GDGT (3.7-55.9 ng/g sed) than samples from south (Xiamen; 251-1020 ng/g sed). iGDGTs and bGDGTs are the predominant components at all sites and account for 17.2-74.3% and 16.1-75.1% of total ether lipids, respectively. The relative abundance of iGDGTs decreases but that of bGDGTs increases with the distance from sea, suggesting a marine vs. terrestrial origin of iGDGT and bGDGTs, respectively. In addition, the methylation index (MIOB/B/SB) of branched GDGTs shows a significant inverse correlation with water content, suggesting that marine waters have a major influence on the microbial communities inhabiting wetland sediment. Such an assumption was confirmed by the distinct lipid pattern of three low water content (<5%) samples collected in an area isolated from tidal flushing. The other isoprenoidal ether lipids, such as iGDDs, OH-GDGTs and OH-GDGTs, have a similar distribution as iGDGTs, indicating a common biological source, so do the corresponding non-isoprenoidal ether lipid series with bGDGTs. The BIT value increases with increasing distance from the sea, which implies that the BIT index can be probably applied to trace past sea level change in costal wetland settings. The reconstructed temperature from TEX86 shows significant offset from observed data, but only little deviation for the MBT/CBT calculated temperature. This suggests that the MBT/CBT has the potential to reconstruct past temperatures in coastal wetland settings.