The aggregation and structure of polar molecules in nonpolar media may have a profound effect on bulk phase properties and transport. In this study, we investigate the aggregation and deposition of water and asphaltenes, the most polar fraction in petroleum fluids. In flow-line experiments, we vary the concentration of water from 500 up to 175 000 ppm and provide the evidence for clear changes in asphaltene deposition. Differential interference contrast (DIC) microscopy and dynamic light scattering (DLS) are used to measure the size of the aggregates. Rheological measurements are performed to get fixed ideas on the structural changes that water induces at different concentrations. This study demonstrates the significant effect of water on asphaltene aggregation and deposition and explores the molecular basis of water-asphaltene interaction. Our aggregate size measurements show that while asphaltene molecules increase the solubilization of water, there is no increase in the aggregate size. Our aggregation size measurements are different from the reports in the literature.