Photodynamic antimicrobial chemotherapy (PACT), employing a combination of light and natural photosensitizer molecules such as curcumin, has been accepted as a safe modality for removing aquatic pathogens which cause diseases such as cholera in humans and vibriosis in aquatic animals. Curcumin and its photodegradation products are generally considered as safe to animals, but the impact of reactive oxygen species (ROS) generated by these products on the growth and survival of organisms at a cellular level has not been studied in detail. The ROS generated by curcumin on photoexcitation using blue light (λmax 405 nm, 10 mW cm−2) disinfects more than 80% of free-living Vibrio spp. in the rearing water of Penaeus monodon. However, it is less effective against Vibrio spp. colonized inside P. monodon because the carapace of the animal prevents the transmission of more than 70% of light at the 400–450 nm range and thus reduces the formation of ROS. The influence of curcumin and photoexcited curcumin on the microbiome of P. monodon were revealed by nanopore sequencing. The photoexcited curcumin induced irregular expression of genes coding the moult-inhibiting hormone (MIH), Crustacean hyperglycaemic hormone (CHH)), prophenoloxidase (ProPO), and crustin, which indicates toxic effects of ROS generated by photoexcited curcumin on the neuroendocrine and immune systems of crustaceans, which could alter their growth and survival in aquaculture settings. The study proposed the cautious use of photodynamic therapy in aquaculture systems, and care must be taken to avoid photoexcitation when animals are experiencing moulting or environmental stress.