Functionalized Multiwall carbon nanotubes (f-MWCNT) is gaining attention because of the range of their applicability in biological sectors. However, it may harm aquatic life and human health. The present work assesses the effect of shear and non-shear forces, and various physical chemical parameters like pH (5, 7, and 9), ionic strength (10, 50, and 100 mM), and humic acid (0.1, 1, and 10 mg/L) on the transport of f-MWCNTs. It is observed that when the shear forces were applied, the physical chemical factors, pH, ionic strength, and humic acid can substantially impact the transport of f-MWCNT. Notably, shear forces at 100 and 400 rpm significantly improved the colloidal stability of f-MWCNT in the aqueous medium, while without shear forces, the aggregation of f-MWCNT increased significantly resulting in decreased transport. Calculations of the Derjaguin–Landau–Verwey–Overbeek (DLVO) interaction energy profile agreed well with the experimental results. Additionally, the transport of f-MWCNTs was studied using various real water systems, including river, lake, groundwater, and municipal drinking water. This study considerably advances our knowledge of different physical, chemical, and environmental factors affecting transport of-MWCNTs in static and dynamic aquatic environments.