Another consequence of the exploitative use of water resources is the destruction of mangrove forests and the fragmentation of the habitats of endangered species. The United Nations Convention on International Trade in Endangered Species of Wild Flora and Fauna listed 189 endangered species in China among the 740 in the world.

Sand content is quite high in the Yellow River. In the dry season, sand rises and flies up with the wind and soil desertization becomes severe. In addition, the River's dri-up directly reduces the quantity of water for farmland irrigation. The supply of ground water decreases while the exploitation quantity of ground water increases. The results would include a deep crescent of ground water, a decrease of land evapo-transpiration, local climate drying, soil desertization, a reduction of biotic population and a simplification of biocommunity structure.

Another serious problem confronted in the Yellow River is nitrogen contamination. A study found that, with an increase in economic activities in the Yellow River's upper basin, the nitrogen concentration in the tributaries increased. This, in turn, increased the nitrogen concentration of the mainstream from the upper and lower reaches. Secondly, nitrogen in the River water was mainly attributed to point sources. And thirdly, the ammonium nitrogen and total inorganic nitrogen content of the River water increased significantly from 1980 to 1999. This was a time when water discharge and nitrogenous fertilizer application in the Yellow River catchment increased.

It is not only contamination but also the overgrowth of microorganisms, which troubles the Yellow River. Harmful algae blooms or HABs or red tides refer to the discoloration of surface water, often coastal. This is the result of the overgrowth or high concentration of microorganisms. Some of these microorganisms can be toxic and, thus, can kill marine animals on a massive scale. Statistics revealed that HABs have been fast increasing in the coast of China since the 70s. In 2003, HABs were believed to cover a total area of 14,550 kilometers. This magnitude can mean a direct economic loss of 42.81 RMB. These HABs present as a growing problem to fisheries, coastal ecosystems, aquaculture and public health in China's coastal areas.

The Yellow River remains the most important water resource for Northwest China and north China. It is the river in China, which has been subjected to the strongest influence of human activities. With brisk economic spurts and the expansion of population along the River basin, waste water release has increased in unexpected and unprecedented levels. In contrast, the runoff in the lower reaches has rapidly decreased. The River frequently dries up as a consequence. When the runoff is reduced, the ratio of waste water to runoff goes up. The River's purification capability also decreases along with the aquatic environmental capacity. Water pollution in the Yellow River basin...

In the middle and lower reaches, the pollutant concentration has exceeded the lethal concentration for fishes. It has been reported that almost all species of fish have become extinct except in some dams and river sources. (Gao Yan-Chun 1998)
The relative endowment of land and water in the region has also turned scarce. For each crop, the production technology employed must exhibit constant elasticity of substitution or CES between inputs. In the lower Yellow River basin irrigation systems, crops were mainly irrigated with pumped groundwater. Seepage from irrigated fields was an important source of recharge to lowland groundwater. But too much of it would reduce irrigation water-use efficiency. It would then result in shallow ground water tables, which would cause secondary soil salinisation. When there is insufficient recharge to go to lowland groundwater, deep ground water tables could increase the cost of ground water abstraction. It could even lead to overdraft conditions. Sustainable irrigation is, thus, the key factor in the control of the ground water table.