Abstract: Water resources and environmental issues in the Aral Sea Basin of Central Asia are global concerns. In this study, the water quality variables (i.e., basic physical and chemical attributes, different forms of nutrients, other elements, cations, and anions) from 21 sampling sites in the middle and lower reaches of Aral Sea Basin were measured in 2019 to explore water environmental variations and their causes. Spatial variation in 20 water quality variables was investigated, and the representative water quality types, spatial differences, and their causes were identified via multivariate analysis methods (i.e., principal component analysis and cluster analysis). Furthermore, the effects of land cover on the spatial variation in water quality types were explored. The results showed that: 1) the values of electronic conductivity (EC) and total dissolved solids (TDS) increased from the middle to the lower reaches, and the highest values were in the Aral Sea. This indicates that the concentrations of anions and cations increased from the middle to the lower reaches. For the nutrient variables, high phosphorous concentrations were in the middle reaches of Amu Darya, and high nitrate-nitrogen concentrations were in the Syr Darya. For the different forms of carbon, the highest concentrations were in the Amu Darya, particularly in the delta area of lower reaches. 2) The water quality at all sampling sites can be divided into three water quality types according to the similarity classification of water quality variables. The first type had low concentrations for most water quality variables, which were distributed in the middle reaches of Syr Darya and the Aral Sea. The second type had high concentrations of different forms of nitrogen and phosphorus, which were distributed in the middle and lower reaches of Amu Darya. The third type had high concentrations of carbon, anions, and cations, which were distributed in the Aral Sea. The water quality concentrations of the first and second types were mainly due to rock weathering processes on bare land, and the anions and cations were mainly derived from the weathering of silicates and evaporites. The concentrations of the third type were mainly due to the evaporation and crystallization processes of a dry climate, and the anions and cations were mainly derived from the weathering of silicates and evaporites, which may also be affected by carbonate weathering. 3) With an increase in the buffer zone radius for each sampling point (0.5 km to 10 km), the significant land cover changed from bare land to water, shrubland, grassland, mixed farmland, and vegetation for the first water quality type; the most significant land cover was water. There were no significant relationships between the second water quality type and land cover. For the third water quality type, the significant land cover changed from water to water, mixed farmland, and vegetation—the most significant land cover was water. Therefore, spatial variation in the water quality variables was mainly affected by the local climate conditions (i.e., climatic drought and intensive evapotranspiration) and the mainland cover types (i.e., bare land, water, farmland, grassland, and urban). To improve the water environmental conditions in the middle and lower reaches of Aral Sea Basin, stream flow should be increased to recharge the Aral Sea and weaken the evaporation and crystallization processes in the lower reaches of Aral Sea. Vegetation restoration and a return of farmland to forest and grassland should also be strengthened in the riparian zone, particularly in the middle and lower reaches of Amu Darya and Syr Darya and the Aral Sea.