Environmental contamination caused by inorganic compounds is a major problem affecting soils and surface water. Most remediation techniques are costly and generally lead to incomplete removal and production of secondary waste. Nanotechnology, in this scenario with the zero-valent iron nanoparticle, represents a new generation of environmental remediation technologies. It is non-toxic, abundant, cheap, easy to produce, and its production process is simple. However, in order to decrease the aggregation tendency, the zero-iron nanoparticle is frequently coated with chemical surfactants synthesized from petrochemical sources, which are persistent or partially biodegradable. Biosurfactants (rhamnolipids), extracellular compounds produced by microorganisms from hydrophilic and hydrophobic substrates can replace synthetic surfactants. This study investigated the efficiency of a rhamnolipid biosurfactant on the aggregation of nanoscale zer-valent iron (nZVI) and its efficiency in reducing nitrate in simulated groundwater at pH 4.0. Two methods were tested: 1) adding the rhamnolipid during chemical synthesis and 2) adding the rhamnolipid after chemical synthesis of nZVI. Scanning electron microscopy field emission, X-ray diffractometry, Fourier transform infrared spectroscopy, thermogravimetric analysis, Dynamic Light Scattering, and zeta potential measurements were used to characterize bare nZVI and rhamnolipid-coated nZVI. The effects of the type of nZVI and initial NO3 concentration were examined. Nanoscale zer-valent iron with the addition of the rhamnolipid after synthesis achieved the best removal rate of nitrate (about 78%), with an initial nitrate concentration of 25 mg L−1. The results suggest that nZVI functionalized with rhamnolipids is a promising strategy for the in situ remediations of groundwater contaminated by NO3, heavy metal, and inorganic carbon.