Molecular dynamic simulations of Suwannee River fulvic acid (FA) model have been performed explicitly including the solvent water. The analyses of the trajectories showed that phenol groups adjacent to carbonyl groups interact by H-bonding hence promoting a more hydrophobic interior of the FA molecules. Furthermore, carbonyl groups were found to interact with hydroxyl groups especially in a solvated system. The H-bonding interactions induced on FA aggregation have been analyzed for a cluster composed of 7 monomers suggesting that H-bonding between FA molecules does not play an important role in the aggregation process. Some results also suggests that FA molecules in aggregates are bridged by water molecules.