The main aim of this research was to determine the physiological response of the submerged macrophyte Vallisneria natans (V. natans) to black water with a foul odor. V. natans was chosen as the experimental plant species to investigate the morphological response and ecophysiological adaptation methods in response to varying light depths and black-odorous water. V. natans was planted in tap water (D), two types of black-odorous water (E and F), and under three distinct light conditions (low light, medium light, and high light). In the high-light condition with black-odorous water (E), the biomass content of V. natans declined from 1.78 g on the 14th day to 1.49 g on the 28th day, demonstrating that the black-odorous water inhibited the growth of V. natans. Under the stress of black-odorous water, the chlorophyll content of V. natans increased greatly in the early period but reduced during the latter experimental period. However, on the 21st day, maximum chlorophyll content of 1.30 mg/g (E) and 1.18 mg/g (F) was observed. In addition, the malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activity was monitored and reported under black-odorous water stress in V. natans. The experimental results of this work demonstrated conclusively that odorous black water exerts a certain stress on the physiological development of V. natans. Future research should incorporate the evaluation of several plant species and vary the process and environmental conditions to produce field-relevant, dependable results.