Attempts to control massive proliferations of invasive alien aquatic plants (IAAP) are often ineffective. A renewed interest for dye treatment is emerging aiming to control the submerged macrophyte Myriophyllum heterophyllum in France. We aimed to understand the effects of dye on this plant knowing about its adaptation to low light. In a 2 × 2 factorial design experiment, we assessed the effect of a dye mixture based on Brilliant Blue (E133) and Allura Red (E129) at high and low light intensities on light quantity and quality and how this might affect the plant's performance by measuring morphological and physiological traits. A multivariate analysis identified three groupshigh light (HL) plants, plants in high light with dye (HLD) or low light (LL), and low light with dye (LLD) plants. HL plants performed well but showed stress signs, with a reduced main shoot length, a higher leaf dry matter content (LDMC) and a lower nitrogen content (N), not observed in plants grown in HLD or LL. HLD and LL plants exhibited a comparable total length growth rate to those in HL, but had lower LDMC and higher N contents. LLD plants performed poorly with the lowest growth and signs of physiological stress. Dye-induced changes in light quality only marginally affected the absorbance range of chlorophyll b, which apparently did not affect photosynthesis. Commercially available dyes currently used to control nuisance aquatic plants thus seem to have little or no effect on submerged macrophytes. The presence of dye may exacerbate negative effects of very low light intensities on the plant's growth. However, these very low intensities would only be reached during high-water levels or in winter, periods where the dye would rapidly be diluted. During summer, however, the application of dye may protect the plant from damaging light intensities and thus not be a good management strategy to control low light adapted invasive submerged macrophytes.