Water is an important resource for the development of the economy and has a significant influence on maintaining regional ecological balance. Spatial patterns of water quality methods using pH, electrical conductivity (EC), mineralization, and total salt content were examined at 62 sites in and around the Ebinur Lake area. The results of the water quality analysis showed a seasonal variation in pH, EC, mineralization and salt contents between the wet and dry seasons of 2014: (1) Overall, pH showed obvious crisscross pattern; EC, mineralization and total salt showed the large difference between the wet and dry season, high values were recorded around Ebinur Lake, and lower values in farm lands and Haloxylon forests; (2) analysis of spatial autocorrelation of the water quality showed the high-high aggregation(HH) of pH was mainly concentrated in the northern part of the Ebinur Lake and low-low aggregation (LL) was mainly in the southern part. Along the periphery of Ebinur Lake to the Haloxylon forest, EC, mineralization, and salt content decreased with HH- low-high aggregation (LH)-LL transformation per height of the terrain; (3) the relationship between water quality parameters and land use/cover types showed that the influence of forest-grassland, saline soil, and farm land on water quality is relatively significant; (4) to study the changes of water quality, we used farm land, forest-grassland, salinized land, and abandoned (dormant) land to establish an optimized multiple linear regression model with water quality parameters. The correlation coefficients of R were 0.58, 0.72, 0.74, and 0.71, respectively. These indicated the optimal fitting model is a better method for analysis. In summary, this study showed the water quality variations among different land use/cover in the desert region (Ebinur Lake area) can be used for comparison with other desert environments.