Abstract: With the increasing attention paid to groundwater contamination issues, the increasing demand was needed for small-scale site contamination hydrogeological work. The site contamination hydrogeological work has some particularities, which includes small scale, high resolution, and not only studying of contamination processes with the source leakage, but also studying of contaminant removal under the remediation state. Especially the transportation and reactions in the aquifer for in situ injected fluids (gases, liquids and microbes) of remediation agents need to be concerned greatly. The traditional large-scale hydrogeological work is difficult to meet the special needs above, therefore, it is necessary to propose “site contamination hydrogeology” for site-scale groundwater pollution risk management. This paper focuses on the characterization of stratigraphic media and pollution plumes in small-scale contaminated site, quantitative description of the pollutant-water-rock reactions, and the role and influence of pollutants in heterogeneous strata in multiphase systems. Finally, the main research content and key issues for site contamination hydrogeology were proposed, including: high-resolution characterization of sites at small scales, quantitative description of the physical, chemical, and biological reactions of pollutants in the underground environment during pollution and remediation processes, the migration and transformation of pollutants at the site scale in underground environmental media, transport and reaction of remediation agents (additives) in underground environments, and the pollution control and remediation in heterogeneous and low-permeability formations.