Treated wastewater (TWW) irrigation is increasingly used in arid regions, and its effects on soil salinity are well documented. However, its influence on soil carbon fractions, aggregation, and stable carbon (delta C-13) and nitrogen (delta N-15) isotopes remains poorly understood. This study evaluated the impacts of TWW irrigation on soil total carbon (TC), soil organic carbon (SOC), active carbon (AC), inorganic carbon (IOC), water-stable aggregates (WSA), delta C-13, delta N-15, and aggregate-associated carbon and nitrogen isotopes across multiple soil depths. Compared to freshwater (FW), TWW significantly increased AC at 0-15, 15-30, and 30-45 cm by 16.8%, 23.0%, and 32.4%, respectively, and enhanced SOC by 31.7% at 45-60 cm depth. The >2 mm WSA increased by 16.7% and 48.9% at 0-15 and 30-45 cm, respectively, under TWW irrigation. TWW also enhanced aggregate-associated carbon at depths of 0-15 and 15-30 cm and enriched delta N-15 at depths of 30-45 and 45-60 cm. In contrast, aggregate-associated delta C-13 decreased at 30-60 cm, and delta C-13 values across aggregate fractions were consistently lower than bulk soil at depths of 15-60 cm. Variations in SOC and AC were over 30% greater in subsoil than topsoil, whereas delta C-13 and delta N-15 showed no comparable depth trend, indicating a decoupling between soil carbon accumulation and organic matter quality. Structural equation modeling further revealed that soil total carbon, delta C-13, and delta N-15 jointly act as dominant drivers of WSA, highlighting that aggregate stabilization under TWW irrigation is governed by integrated carbon quantity and transformation processes. Overall, TWW irrigation enhances subsoil carbon accumulation and aggregate stability while influencing soil isotopic composition, revealing new insights into soil carbon dynamics in arid agroecosystems.