The interactions of bacteria with organic matter affects applications ranging from natural processes such as bacterial transport in the subsurface and in situ bioremediation, to engineered processes such as bioaugmentation and bacterial inactivation with antimicrobial peptides. In the environment, natural organic matter (NOM) is a complex mixture that includes identifiable compounds such as proteins and polysaccharides, but is generally defined operationally into groups such as humic and fulvic acids. This work describes how atomic force microscopy (AFM) can be used to characterize and quantify the interfacial forces between microbes and organic matter-coated surfaces. A model polymer, poly(methacrylic) acid, was chosen as a simple model for NOM, due to its highly charged nature and presence of carboxylic groups. The way that the model NOM interacted with bacteria was compared with the behavior of Suwanee River Humic Acid and a Soil Humic Acid. Based on AFM measurements of adhesion forces between bacteria and an NOM-coated probe, PMA was not a good model for the way bacteria interacted with the humic acids. To try and develop a more fundamental understanding of bacterial interactions with organic molecules, we also quantified the adhesion forces between bacteria and model proteins (BSA, con A), and determined that these interactions are dependent on bacterial LPS structure. Finally, new results are presented on the binding between bacterial LPS and peptides having antimicrobial properties.