In the development of nanoenabled technologies for large-scale water treatment, immobilizing nanosized functional materials into the confined space of suitable substrates is one of the most effective strategies. However, the intrinsic effects of nanoconfinement on the decontamination performance of nanomaterials, particularly in terms of structural modulation, are rarely unveiled. Herein, we investigate the structure evolution and decontamination performance of iron (hydr)oxide nanoparticles, a widely used material for water treatment, when confined in track-etched (TE) membranes with channel sizes varying from 200 to 20 nm. Nanoconfinement drives phase transformation from ferrihydrite to goethite, rather than to hematite occurring in bulk systems, and the increase in the nanoconfinement degree from 200 to 20 nm leads to a significant drop in the fraction of the goethite phase within the aged products (from 41% to 0%). The nanoconfinement configuration is believed to greatly slow down the phase transformation kinetics, thereby preserving the specific adsorption of ferrihydrite toward As(V) even after 20-day aging at 343 K. This study unravels the structure evolution of confined iron hydroxide nanoparticles and provides new insights into the temporospatial effects of nanoconfinement on improving the water decontamination performance.