Understanding the variation of soot deposit properties in diesel particulate filters is necessary for their real-life modeling and onboard control. In this study, the effect of exhaust mass flow rate and particle agglomerate size on the soot layer permeability and density was investigated experimentally and analyzed using a well-validated model. A bare and a coated diesel particulate filter were loaded at five different engine operating points, specially selected to explore these effects in a heavily used part of the diesel engine map. Particle emissions were characterized in terms of particle agglomerate size distribution and primary particle diameter, while soot layer permeability and density were estimated indirectly by fitting the model to the pressure drop recordings. To this end, an automatic calibration procedure was applied to obtain values in a consistent and repeatable manner. The results showed considerable variation in both permeability and density. Furthermore, some trends could be identified after depicting the particle characterization data and soot layer properties in contour plots. Increased permeability appeared at the engine operating point with high flow rate and large particle agglomerate size. Lower density was obtained at the operating points with large particle agglomerate diameter.