Nanoparticles aggregation is considered, by the heat transfer community, as one of the main factors responsible for the observed enhancement in the thermal conductivity of nanofluids. To gain a better insight into the veracity of this claim, we experimentally investigated the influence of nanoparticles aggregation induced by changing the pH value or imposing a magnetic field on the thermal conductivity of water-based nanofluids. The results showed that the enhancement in thermal conductivity of TiO2–water nanofluid, due to pH-induced aggregation of TiO2 nanoparticles, fell within the ±10% of the mixture theory, while applying an external magnetic force on Fe3O4–water nanofluid led to thermal conductivity enhancements of up to 167%. It is believed that the observed low enhancement in thermal conductivity of TiO2–water nanofluid is because, near the isoelectric point (IEP), the nanoparticles could settle out of the suspension in the form of large aggregates making the suspension rather unstable. The magnetic field however could provide a finer control over the aggregate size and growth direction without compromising the stability of the nanofluid, and hence significantly enhancing the thermal conductivity of the nanofluid.