New Mexico Aquifer Assessment Act of 2006 - Directs the Secretary of the Interior, acting through the Director of the United States Geological Survey (USGS), to conduct a study of water resources in New Mexico, to include: (1) a survey of groundwater resources and a characterization of surface and bedrock geology; and (2) the Estancia Basin, Salt Basin, Tularosa Basin, Hueco Basin, and middle Rio Grande Basin.