Humic acid-coated goethite nanoparticles (HA-GoeNPs) have been recently proposed as an effective reagent for the in situ nanoremediation of contaminated aquifers. However, the effective dosage of these particles has been studied only at laboratory scale to date. This study investigates the possibility of using HA-GoeNPs in remediation of real field sites by mimicking the injection and transport of HA-GoeNPs under realistic conditions. To this purpose, a three-dimensional (3D) transport experiment was conducted in a large-scale container representing a heterogeneous unconfined aquifer. Monitoring data, including particle size distribution, total iron (Fetot) content and turbidity measurements, revealed a good subsurface mobility of the HA-GoeNP suspension, especially within the higher permeability zones. A radius of influence of 2 m was achieved, proving that HA-GoeNPs delivery is feasible for aquifer restoration. A flow and transport model of the container was built using the numerical code Micro and Nanoparticle transport Model in 3D geometries (MNM3D) to predict the particle behavior during the experiment. The agreement between modeling and experimental results validated the capability of the model to reproduce the HA-GoeNP transport in a 3D heterogeneous aquifer. Such result confirms MNM3D as a valuable tool to support the design of field-scale applications of goethite-based nanoremediation.