To understand the implications of archaeological site recording practices and associated inventories for studying Indigenous persistence after the arrival of Europeans, we examined the documentary record associated with nearly 900 archaeological sites in Marin County, California. Beginning with the first regional surveys conducted during the early 1900s and continuing into the present, the paper trail created by archaeologists reveals an enduring emphasis on precontact materials to the exclusion of more recent patterns of Indigenous occupation and land use. In assessing sites occupied by Indigenous people from the late sixteenth through the mid-twentieth centuries, we discuss how the use of multiple lines of evidence—including temporally diagnostic artifacts, chronometric dating techniques, and historical documentation—may help illuminate subtle but widespread patterns of Native presence that have been obscured by essentialist assumptions about Indigenous culture change. Our findings further reveal the shortcomings of traditional site recording systems, in which archaeologists typically categorize sites within the prehistoric-protohistoric-historic triad on the basis of commonsense decisions that conflate chronology with identity. Instead, we argue for recording practices that focus specifically on the calendric ages of occupation for any given site.