Oxygen Levels
Low-oxygen levels in soil is due to the length and depth of flooding in the area. Plants need oxygen and must adapt to less oxygen or develop storage cells in stems and leaves that transport the oxygen to the roots.
Wind and Sunlight
Plants in estuaries must contend with varying wind exposure and unpredictable sunlight. This is due to the tidal cycle in which tide water flows into the estuary two times a day and then out to the sea, leaving, in many cases, the plant life exposed to the elements for hours until the next cycle begins.
Waves and Currents
Storm waves and strong currents determine what plants can survive in which parts of the estuaries. Plants need deep, strong root systems to withstand the intense currents and strong ocean storm waves that travel miles inland up the estuary channel.
Salinity
A plant's toleration of varying levels of salt, determines where it can flourish in different areas of estuaries.
The salinity of the water in estuaries changes quickly during the tide cycle so plants called euryhaline, such as the mangrove trees, must be able to tolerate the rapid change.
Other plants such as the smooth cord grass have adapted to the saline environment by removing salt from the water through special filters found on their roots and releasing the excess salt out their leaves.
Some parts of the estuary nearer to the ocean are constantly covered in saltwater and therefore, when the salt water contains more than 40 parts per thousand of dissolved salts, hyperhaline plants, or those that live in high salinity water such as the seagrass and eelgrass, can survive.
Part of the Food Web
Marsh plants, eel grass and bottom-dwelling algae are the basis of the estuary food web, not so much when they are alive, but when they die and are coated with microorganisms such as protozoa. Small invertebrates eat these microorganisms and larger fish, in turn, eat these small animals.