Recently developed wet mills (bead mills) have been shown capable of dispersing nanoparticle aggregates into primary particles in suspension, even with nanoparticles with primary particle radii as small as 5nm and at high nanoparticle volume fractions (>1%). However, to date what has not been examined is the change in aggregate morphology during milling itself, i.e. it is not clear if wet milling simply fragments aggregates into smaller, similarly structured entities, or if milling can simultaneously lead to aggregate restructuring. Here we develop and apply methods to examine the change in morphology in titania and alumina nanoparticle aggregates (primary particle radii of ~8.25nm and 7.20nm, respectively) during wet milling with a Kotobuki Industries UAM-015 wet mill. Specifically, via nanoparticle tracking analysis (NTA) with a Nanosight LM-14 and simultaneous viscosity measurements, we characterized the hydrodynamic radius distribution functions and average intrinsic viscosities of both titania and alumina aggregates milled at 1% volume fraction in water. With NTA we found that for both particle types, milling led to a reduction in hydrodynamic radii. Conversely, the average intrinsic viscosity of titania decreased, while it increased for alumina with increasing milling time. By assuming aggregates were quasifractal in morphology (and hence characterized by the number of primary per particles per aggregate, the pre-exponential factor, and the fractal dimension) and by using Monte Carlo based techniques to link quasifractal aggregate descriptors to both the hydrodynamic radius and the intrinsic viscosity for an aggregate, measured hydrodynamic radius distribution functions and average intrinsic viscosities were used to infer titania and alumina aggregate quasifractal descriptors as functions of milling time. Through this analysis we found that both particle types were initially dense aggregates (fractal dimensions >2.9), and for titania milling did not alter aggregate morphology (i.e. titania aggregates remained dense). However, alumina aggregates were found to decrease in fractal dimension with increasing milling time, reaching a value near 1.6 after 180minutes of milling. Such chain-like structures give rise to an increase in suspension viscosity despite the fact that alumina aggregate size decreased with milling. Overall, we show that depending on the particle material (and surfactant employed), milling may simultaneously lead to aggregate size reduction and restructuring, and may be a viable approach to the production of controlled morphology aggregates.