The large amount of agricultural land development in the irrigation area of the lower Amudarya has led to a greater amount of water resources being introduced into the irrigation area. The high groundwater level in the irrigation area and the unreasonable management of water resources have led to the deterioration of the regional ecological environment. In the context of global climate change, we used a variety of trend analysis methods and correlation analysis methods and found that human activities are the main factors affecting regional annual groundwater level changes and annual groundwater level fluctuations, accounting for 67.6% and 78.9%, respectively. These factors have led to a high temporal and spatial heterogeneity of the regional groundwater from 1990 to 2020: the multiyear rate of change at various points in the region ranges from -0.054 m/a to 0.098 m/a, and the groundwater level in the entire area is rising at a rate of 0.015 m/a. Under the scenario of increasing groundwater level volatility, the continuously rising water level requires us to consider whether this state will cause harm to the future area, so we used the capillary method to define the regional ecological water level as 1.78-2.78 m. When exploring its relationship with regional groundwater, it was found that starting in March, 72.2% of the regional groundwater level exceeded the ecological water level by an average of 0.38 m, and by July, 83.5% of the region exceeded the ecological water level by an average of 0.98 m; furthermore, the highest point was only 0.5 m from the ground. Under the future changing trend of regional groundwater in the future, such results will cause a further deterioration of regional ecology, and sustainable groundwater exploitation methods with the goal of maintaining the ecological water level should urgently be proposed.