Increased urbanization has caused problems such as increasing water consumption and the continuous deterioration of the groundwater environment. It is necessary to consider the groundwater quality in the water resource optimization system and increase the rate of reclaimed water development to reduce the amount of groundwater exploitation and achieve sustainable development of water resources. This study used the Daxing District, a region of Beijing’s southern plain, as an example to evaluate water quality by analyzing water quality data of surface and groundwater from 2012 to 2016 and actual water-use schemes from 2006 to 2016. Three groundwater extraction modes were set up based on NO3–N concentrations, water resources were optimized under three extraction modes, and water resource optimization schemes were determined based on the improved connection entropy. The results show that (1) the surface water quality was poor, and the proportion of V4 type water in the indexes of NH3–N and chemical oxygen demand (COD) was the largest. The surface water can only be used for agricultural irrigation. The pollution sources contributing most to NH3–N and COD were domestic and agricultural pollution sources. (2) The groundwater quality was good. The NO3–N index was primarily type I–III water, accounting for 95.20% of the total samples. Severe NH3–N pollution areas were mainly in the northern region, and most regional groundwater can be used for various purposes. (3) Taking 2016 as an example, three groundwater exploitation modes were set to optimize water resource allocation, and the results showed that the rate of groundwater development and NO3–N pollution decreased significantly after optimization. (4) Connection entropy is an evaluation method that combines connection numbers and entropy, including identify, difference, and opposition entropy. As connection entropy being a kind of complete entropy, which can reflect the difference of the system in different states, based on the improved connection entropy, the connection entropies of optimal water resource allocation and actual water-use schemes were calculated. The connection entropy of groundwater exploitation mode 3 was less than that of groundwater exploitation modes 1 and 2 and actual water-use schemes from 2006 to 2016. Therefore, exploitation mode 3’s water resource optimization scheme was recommended. In the paper, satisfactory results have been obtained. As a kind of complete entropy, connection entropy has great research value in dealing with complex hydrological problems. This study’s research methods and outcomes can provide methodological and theoretical lessons for water management in freshwater-deficient areas.
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