Disinfection by-products (DBPs) such as chloroacetic acids (CAAs) and N-Nitrosodimethylamine (NDMA) are prevalent pollutants in surface waters, particularly with the increasing use of chlorine-based disinfectants. The entry of these DBPs into water bodies may increase accordingly, posing ecological risks to aquatic life. To assess the toxic effects of CAAs and NDMA on submerged macrophytes, Vallisneria natans was exposed to different concentrations of CAAs (1.0, 10.0, and 100.0 μg L⁻¹) and NDMA (0.1, 1.0, and 10.0 μg L⁻¹). A RI value of <1 indicates that simultaneous exposure to CAAs and NDMA can produce an antagonistic effect. Both CAAs and NDMA adversely affect the photosynthetic system of plants. In the NDMA treatment group, chlorophyll a content decreases with increasing concentration, accounting for 96.03%, 60.80%, and 58.67% of the CT group, respectively. Additionally, it effectively triggers the plant’s antioxidant response, with significant increases in SOD, POD, and GSH levels. Among these, the combined treatment group AN2 (10 + 1 μg L⁻¹) showed the most significant change in SOD activity, reaching 3.57 times that of the CT group. Ultrastructural changes also revealed stress responses in leaf cells and damage to organelles. Furthermore, metabolomics provided insights into the metabolic responses induced by CAAs or NDMA in V. natans leaves, where the composition and metabolism of lipids, fatty acids, cofactors and vitamins, amino acids, nucleotides, and some antioxidants were regulated, affecting plant growth. This study provides preliminary information for the ecological risk assessment of submerged plants by complex contamination with the disinfection by-products CAA and NDMA.