Compound-specific isotope analysis (CSIA) is an established tool to study the fate of legacy groundwater contaminants but is only emerging for nonconventional contaminants, e.g., nitro- and amino-substituted chlorobenzenes that are widely used as industrial feedstock and the target of this work. To date, CSIA of the target compound groups used special combustion interfaces and the potential matrix interferences in environmental samples has not been assessed. We validated CSIA methods for δ13C, δ2H, and δ15N of four analytes from each chemical group and developed a solid-phase extraction (SPE) method to minimize matrix interferences during preconcentration of complex aqueous samples. The SPE recovery was >80% and the method quantification limits of SPE-CSIA for δ13C, δ2H, and δ15N were 0.03-0.57, 1.3-2.7, and 3.4-10.2 μM aqueous-phase concentrations, respectively, using 2 L of spiked MQ water. The SPE-CSIA procedure showed negligible isotope fractionation for δ13C (≤0.5‰), δ15N (≤0.5‰), and δ2H (≤5‰ for nitroaromatics and ≤10‰ for aminoaromatics). In addition, solvent evaporation, water sample storage up to 7 months, and SPE extract storage for 1.5 years did not change analytes' δ13C signatures beyond ±0.5‰. However, to avoid significant δ2H and δ15N fractionation of aminoaromatics, cartridge breakthrough should be avoided and SPE preconcentration must be conducted at pH > pKa + 2. Application of the method at a contaminated site showed excellent precision, at ≤0.3‰ for C and N, and ≤1.5‰ for H. The methods validated here now allow the use of multielement CSIA to track the environmental fate of nitro- and amino-substituted chlorobenzenes in complex aqueous samples.