Effects of four benzoquinoline isomers on the filtration rate of the zebra mussel (Dreissena polymorpha) were analyzed, to study the effect of minor differences in chemical structure on adverse biological effects. Filtration rates were measured after 48 h of exposure to different concentrations of acridine, phenanthridine, benzo[f]quinoline, and benzo[h]quinoline in the water. The 50% effective concentration (EC50) values for filtration rate of the four isomers differed significantly. Effects increased in the order benzo[f], -[h], -[b], and -[c]quinoline, and the difference between the most toxic isomer and the least toxic isomer amounted to a factor of 30. Attempts were made to relate these differences in toxicity to the structure of the isomers. Size- or topology-related molecular descriptors provided insufficient resolution to distinguish between the benzoquinoline isomers, and none of the electronic descriptors separately provided a significant correlation with the observed effects. In an alternative approach, molecular shape, accessibility, and minimum agent-macromolecule distance were used to represent repulsive and attractive forces between the benzoquinoline isomers and biological membranes. This approach could tentatively explain the observed effects and is supported by a high correlation between the EC50 data and the reversed-phase C18-HPLC behavior of the benzoquinolines (k(0)), which is likely to be governed by similar processes.