Natural organic matter (NOM) is ubiquitous in soil and groundwater and its aqueous complexation with various inorganic and organic species can strongly affect the speciation, solubility and toxicity of many elements in the environment. Despite significant geochemical, environmental and industrial interest, the molecular-scale mechanisms of the physical and chemical processes involving NOM are not yet fully understood. Recent molecular dynamics (MD) simulations using relatively simple models of NOM fragments are used here to illustrate the challenges and opportunities for the application of computational molecular modeling techniques to the structural, dynamic, and energetic characterization of metal-NOM complexation and colloidal aggregation in aqueous solutions. The predictions from large-scale MD simulations are in good qualitative agreement with available experimental observations, but also point out to the need for simulations at much larger time and length scales with more complex NOM models in order to fully capture the diversity of molecular processes involving NOM.