Predicting the partition behavior of bifunctional molecules from their molecular structure is a challenge because the combination of two or more functional groups often has nonadditive effects. Data presented here and in the literature reveal that isomers of bifunctional compounds can exhibit partition constants that differ by several orders of magnitude. These effects are not limited to compounds with intramolecular H-bonds. For aliphatic molecules, large effects are found for diones and diesters but not for dioles. For aromatic molecules, large effects are found for compounds with intramolecular H-bonds and also for p-isomers with a strong delocalisation of pi-electrons over both functional groups as in p-nitroaniline and p-nitrophenol. Interestingly, these nonadditive effects apply not only to the specific interactions but also to the van der Waals interactions of a molecule. This diversity of possible nonadditive effects makes it difficult to predict partitioning of such polyfunctional molecules. Our results suggest that successful models require either an extensive number of correction factors or a quantum chemical approach. Predicting partitioning of bifunctional molecules to environmental systems might face an additional complication. Unlike with solvents, steric limitations of natural phases may prevent them from forming multiple H-bonds with bifunctional molecules. Our experimental results, however, indicate that this situation does not occur, as the H-bond-interaction behavior of bifunctional molecules in humic matter and on quartz was the same as it was in various solvent systems.