An hypothesis for the structure of dissolved organic matter (DOM) in water is proposed. It is based on previously published humic acid and soil organic matter (SOM) models. Personal computer (PC)-based molecular modeling and geometry optimization of DOM and humic/xenobiotic complexes in vacuo and water were performed using modern PC software in order to determine low energy conformations and to simulate site-specific processes such as trapping and binding of biological and anthropogenic substances. Nanochemistry (10 Οͺ9 m level) allows the evaluation of atomic and molecular space requirements, voids, inter-and intramolecular hydrogen bonds, and interactions with water, metal cations, and xenobiotics. The described modeling approach in general allows hydrophilic and hydrophobic reactions to be examined. Structural, molecular, and environmental properties of DOM and its xenobiotic complexes were determined by quantitative structure-activity relationship software. Focal points were molecular properties, such as solvent accessibility as well as van der Waals surface areas and volumes, partial charges, hydration energy (peptides), hydrophobicity (log P), refractivity, and polarizabilities of humic/xenobiotic complexes were determined. Molecular mechanics calculations show that nonbonded forces (e.g., van der Waals) and hydrogen bonds were the main reasons for temporary immobility of xenobiotic substances retained in DOM. Preliminary experiments to simulate the acidity of water molecules by protonation-enhanced reactions with polar xenobiotics (e.g., hydroxyatrazine) but left nonpolar substances (e.g., DDT) unchanged.