An ecosystem-level study was conducted in the Guandu wetlands in subtropical coastal Taiwan to examine how salinity influences the abundance, diversity, and structure of biotic communities. We surveyed eight permanent study sites, spanning freshwater marshes, to the gate on the dyke, and mesohaline mangroves representing a gradient of the extent of saltwater incursions. Analyses of abiotic variables showed that salinity was the primary determining factor for discriminating habitat types in the wetlands, but communities differed in their sensitivity to salinity. The composition of plant and insect communities was most affected by the salinity gradient, suggesting the utility of these communities for ecological monitoring of saltwater incursions. However, spatial changes in communities at higher trophic levels, including macrobenthos, mollusks, fish, and birds, could not be explained simply by the salinity gradient. Instead, changes in these communities were more relevant to the composition of other biotic communities. Our results show that species richness and diversity of plant communities were higher in the marshes than in the mangroves. Nevertheless, insect communities censused in the mangroves had higher diversity, despite lower abundance and species richness. Macrobenthos surveyed in the mangroves showed higher biomass and number of taxa. Mollusks and fish were also more abundant at sites near the gate compared to the marsh sites. This suggests that maintaining a tidal flux by means of gate regulation is necessary for conserving the spatial heterogeneity and biodiversity of coastal wetlands.