The effective dynamic viscosity was measured in the graphite water-based nanofluids. The shear thinning non-Newtonian behavior is observed in the measurement. On the basis of the best fitting of the experimental data, the viscosity at zero shear rate or at infinite shear rate is determined for each of the fluids. It is found that increases of the particle volume concentration and the holding time period of the nanofluids result in an enhancement of the effective dynamic viscosity. The maximum enhancement of the effective dynamic viscosity at infinite rate of shear is more than 24 times in the nanofluids held for 3 days with the volume concentration of 4% in comparison with the base fluid. A transmission electron microscope is applied to reveal the morphology of aggregated nanoparticles qualitatively. The large and irregular aggregation of the particles is found in the 3-day fluids in the drying samples. The Raman spectra are extended to characterize the D and G peaks of the graphite structure in the nanofluids. The increasing intensity of the D peak indicates the nanoparticle aggregation growing with the higher concentration and the longer holding time of the nanofluids. The experimental results suggest that the increase on effective dynamic viscosity of nanofluids is related to the graphite nanoparticle aggregation in the fluids.