Several research groups have studied new biopesticides which are less toxic to the environment and capable of controlling the vectors of parasitic diseases, especially in aquatic ecosystems. Pest control by photodynamic substances is an alternative to chemical or other measures, with chlorophyll and its derivatives as the most studied substances supported by their easy availability and low production costs. The impact of chlorophyll derivatives on four different species, a small crustacean (Daphnia similis), a unicellular alga (Euglena gracilis) and two species of fish (Astyanax bimaculatus and Cyprynus carpio) were tested under short-term conditions. In addition, the effects of long-term exposure were evaluated in D. similis and E. gracilis. In short-term tests, mortality of D. similis (EC50 = 7.75 mg/L) was most strongly affected by chlorophyllin, followed by E. gracilis (EC50 = 12.73 mg/L). The fish species showed a greater resistance documented by their EC50 values of 17.58 and 29.96 mg/L in C. carpio and A. bimaculatus, respectively. A risk quotient is calculated by dividing an estimate of exposure by an estimate of effect. It indicated that chlorophyll derivatives can be applied in nature to control the vectors of parasitic diseases under short-term conditions, but long-term exposure requires new formulations.