Ecosystem services (ES) are essential for human well-being. However, few studies have investigated the optimization of the management of water resources based on trade-offs of ES in arid areas. In order to solve this problem, four important ES that affect the carbon cycle and water cycle were selected from the regulating ecosystem services (carbon storage (CAS), evapotranspiration (ET)), the supporting ecosystem services (the soil drought index (TVDI)) and the provisioning ecosystem services (groundwater depth (GWD)) in arid areas. The spatiotemporal distribution of these four ES were quantitatively analyzed—using related models—in the Tarim River, situated in a typical arid inland basin, in 2000, 2010, and 2018, in order to determine the fundamental driving factors of change in ES. The results showed that CAS was mainly affected by changes in land use, while ET, TVDI, and GWD were mainly affected by changes in water volume. The unified management of water resources improved the regulating ecosystem services (an initial increase in CAS, followed by a decrease; ET continued to grow from 2000 to 2018), the supporting ecosystem services (TVDI was maintained at 0.69–0.74), and the provisioning ecosystem services (GWD rose 5.77% in 2000–2010, and stabilized at 3.05 m in 2018). The trade-off/synergy relationships of the four ES were further analyzed at different geographical scales through correlation analysis and the trade-off index (RMSD). In different river sections, the ES that affect carbon and water cycles were highly dependent on each other. In areas with high CAS, the groundwater depth was low, and the soil moisture and ET were high. With different land use types, there was a synergistic relationship between CAS and GWD in woodland and grassland areas, and between ET and GWD in farmland areas. This showed that there was still strong competition between natural vegetation and groundwater, represented by woodland and grassland, and the ineffective loss of water resources such as ET through expansion of farmland. Finally, this study innovatively incorporated the results of trade-offs of ES into water resource management. In order to reduce the trade-offs between ES, and to improve ES, to achieve the ecological protection and restoration of desert riparian forests, and to optimize the water resource management in arid areas, different ecological water regulation and control measures were proposed in the high-flow years and the low-flow years of arid areas. This study can provide important scientific references for the improvement of ES and the optimization of the management of water resources in other similar river basins in arid areas.