Invasive alien species can have effect on availability of surface water by changing water table level as is happening in Africa, Australia and Latin America. Biodiversity of coastal and marine waters, notably fish and shellfish, plays a vital role in providing food for many peoples. Healthy coastal ecosystems protect coasts against storms and flooding. Natural vegetation cover in water catchments helps to maintain hydrological cycles, regulating and stabilising water runoff, and acting as a buffer against extreme events, such as, flood and drought.

Vegetation removal results in siltation of catchment waterways, loss of water yield and quality, and degradation of aquatic habitat. Vegetation also helps to regulate underground water tables, preventing dry land salinity which affects vast areas of agricultural lands, at great cost to the community. Wetlands and forests act as water purifying systems. Mangroves trap silt, reducing impacts on marine ecosystems. These services translate into substantial financial benefits. As water flows through wetlands, plant, microbe, and sediment processes strip out nutrients like nitrogen and phosphorus from human settlement. Plants take up these nutrients, incorporate them into root, stem and leaf material.

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Some microbes transform a water soluble form of nitrogen into gaseous nitrogen. Constructed wetlands are designed for removing nutrient and toxins from water. Restoring wetlands to reduced nitrogen loading is considered less expensive than construction of wastewater treatment plants. Rivers carry excessive nutrients from runoff to coastal estuaries. Resulting nutrient-over enrichment causes low dissolved oxygen level, harmful algal blooms and loss of submerged aquatic vegetation. Bivalve molluscs including mussels, clams and oysters act as filtering systems in estuary.

They remove suspended materials and consume algae, addressing the overproduction problem. For centuries, the oyster population of Chesapeake Bay was capable of filtering a volume of water equal to complete volume of the Bay in a three-day period pollution, habitat destruction, overharvesting and other pressure have dramatically reduced oyster population, and thereby greatly diminishing this critical filtering service. With diminished oyster populations, the filtering now takes a year, and waters of the Bay area poorer in oxygen and generally more polluted. Dams and diversion change of natural flow of rivers alters quality of aquatic habitat and causing species loss. Reservoirs destroy former land, plant and animal habitat degrading natural beauty.

In arid regions, reservoirs lead to greater water evaporation resulting in increased salinity. When this water is used for irrigation, salt accumulates in soil, resulting in a decline in crop yields and in extreme cases rendering soil unfit for agriculture.