While environmental fate and transport of nano-sized TiO2 (nTiO2) attracts intensive attention, how physical characters of natural waters, such as water type, temperature, and flowing velocity, impact the mobility of nTiO2 remain unclear now. In this work, ultrapure water, lake water, and sea water were chosen to investigate the aggregation and sedimentation behaviors of nTiO2 under a series of environmental conditions with varying feeding concentration, water temperature, and flow velocity. In general, the results demonstrated poorer stability of nTiO2 in sea water than other water types. After a 7-hour test (initial nTiO2=100mg/L), the nTiO2 hydrodynamic sizes, sedimentation rates, and zeta potentials differed significantly in ultrapure water (545nm, 24%, −30mV), lake water (1374nm, 56%, −16mV) and sea water (2152nm, 87%, −3mV). Meanwhile, the study exhibited significant influences of initial nTiO2 concentration (10–100mg/L) on the behaviors of nTiO2 in sea water and lake water but negligible impact on ultrapure water. Ambient temperature also directly affected the aggregation and sedimentation rates of nTiO2, both hydrodynamic diameters and sedimentation of nTiO2 increased markedly with the rising ambient temperatures (10–60°C). In contrast, increasing water flow velocity (0–0.32m/s) lowered the hydrodynamic diameters and sedimentation rates of nTiO2, although the influence of flowing velocity on the aggregation of nTiO2 was partially reversible.