Human activity has been the major threat to wetlands. Agriculture, industrial development, and urban and suburban sprawl have caused the greatest losses of freshwater wetlands. Agriculture is no longer expanding on the Gulf Coast, and very little of the current loss can be attributed to it. In fact, riceland agriculture, because of the flooding that goes with it, provides some additional wetland habitat not otherwise available. The biggest current source of loss for freshwater coastal wetlands is from urban sprawl. Land subsidence caused by the mining of oil, gas and groundwater has been the primary source of saltwater wetland loss. Subsidence causes the land surface to drop, which can then become flooded if the surface is already very near to sea level. Subsidence-induced flooding has drowned many wetlands, especially in and around large coastal cities such as Houston.

Estuarine wetlands are dependent upon freshwater inflow from rivers. In some estuaries, such as Corpus Christi Bay, there is not enough freshwater inflow to maintain maximum estuarine productivity. The Nueces River, which once flowed down through the marshes of the Nueces River Delta, has been diminished and rerouted and no longer provides much freshwater inflow to the deltaic wetlands.