Because archaeological sites are buried, it is often not possible to gather enough information to determine the eligibility of a site during the Phase I survey. Phase II archaeological testing is used to make a formal Determinations of Eligibility for sites that possess enough integrity to be considered potentially eligible for nomination to the National Register of Historic Places. Typically, testing projects involve digging additional shovel test pits at a closer interval to better define the structure of a site as well as the excavation of square or rectangular test units to determine the site's soil stratigraphy (ie. are there different cultural periods represented at different depths), gather artifacts for dating and functional analysis, and determine the site’s state of preservation. Detailed maps of the site are generated at this phase, which show the locations of shovel tests and test units.

Knowledge of current archaeological research is a critical element at this stage, as archaeological sites are evaluated based on the information they can contribute to regional research. This includes knowledge or review of other archaeological reports as well as interviews with local experts. When historic sites need Phase II testing, archival research is conducted to determine who owned and occupied a particular site and when. Artifacts collected during fieldwork are processed and analyzed in the laboratory at a more intensive level than at the survey stage, since both the fieldwork and analysis must address the site's research potential. A report detailing the results of the work is prepared, making and makes a recommendation on the significance of each site as either eligible or not eligible for the National Register of Historic Places. This report is submitted to the lead federal agency, state agency, and State Historic Preservation Office (SHPO) for review. The final determination of eligibility is made by the lead federal or state agency and SHPO, and in instances where they disagree on a site's significance, the opinion of the Advisory Council on Historic Preservation may be sought.

When archaeological sites are determined eligible as a result of Phase II testing, the National Historic Preservation Act requires that the effects of the project on the eligible resources be "mitigated." Mitigation can be accomplished by avoidance if resources are identified well enough in advance and if the project can be designed around the significant resource. Where eligible archaeological sites cannot be avoided, mitigation can be accomplished through Phase III data recovery.

Phase II site evaluations require the excavation of formal test units to evaluate a site's stratigraphy, cultural components, and integrity. New South Associates' Principal Investigator, Brad Botwick, excavates a test unit at a historic brick factory in the southeast to determine if it meets the criteria of eligibility for nomination to the National Register of Historic Places.