The routine rational design of commercial chemicals with minimal toxicological hazard to humans and the environment is a key goal of green chemistry. The development of such a design strategy requires an understanding of the interrelationships between physical–chemical properties, structure, mechanisms and modes of action. This study develops property-based guidelines for the design of chemicals with reduced chronic aquatic toxicity to multiple standardized species and endpoints by exploring properties associated with bioavailability, narcotic toxicity and reactive modes of action, such as electrophilic interactions. Two simple properties emerge as key parameters that distinguish chemicals in the Low EPA level of concern to three aquatic species from those in the High level of concern – octanol–water partition coefficient, (log P_o–w) and ΔE (LUMO–HOMO energy gap). Physicochemical properties were predicted using Schrodinger's QikProp, while frontier orbital energies were determined based on AM1 and DFT calculations using Gaussian03. Experimental toxicity data used consisted of chronic toxicity thresholds (NOEC) for Daphnia magna reproduction (317 compounds, 504 h-assay) and Oryzias latipes (Japanese medaka, 122 compounds in 336, 504 and 672 h assays) survival, and Pseudokirchneriella subcapitata, a green algae model (392 compounds). Results indicate that 92% of compounds of Low chronic concern have log P_o–w values < 2 and ΔE > 9 eV. Chronically safe compounds to P. subcapitata meet similar criteria – 80% have log P_o–w values < 3 and ΔE greater than 9 eV. Our work proposes design guidelines that can be used to significantly increase the probability that a chemical will have low chronic toxicity, based on the endpoints evaluated, to the three diverse aquatic species studied, and potentially to other aquatic species.