Some marshes are tidal marshes which means that water levels can increase and Salt Marsh Harvest mice are forced to stay on certain parts of the land. Often they are out in the open which means predators have an easy target to prey upon. The extent of this natural damage upon the population of the Salt Marsh Harvest mouse is unknown, however, it is far less than the damage done to the population by humans. In the San Francisco Bay area, the homes of Salt Marsh Harvest mice are being destroyed by humans. The land is developed and the mice are forced off of it.
Ground water pumping by humans causes land subsidence, which causes a change in the vegetation.
Cattails and pickleweed are still present for the mice to live amongst, but the amount of pickleweed, which grows in the marshes and is a part of their habitat, is declining and cordgrass is growing in its place. This has been a major contributor to the loss of the salt marsh harvest mice. With the number of Salt Marsh Harvest mice declining, a drastic plan is needed to save the remaining mice and bring the species' population back up to viable numbers. Currently, there are many programs which are in place to aid in the conservation of the mice. The first and most important program is the Endangered Species Act which was put into place in 1973.