Magnetic, palynological, and paleoecological data indicate that in the Río de la Pasión drainage, one of the most thoroughly investigated areas of the southern Maya lowlands, a refugee population remained in the Laguna Las Pozas basin long after the Classic Maya collapse and the Terminal Classic period, previously identified by archaeologists as eras of near-total regional abandonment. During the Early Postclassic period, ca. A. D. 900 to 1200, agriculturalists colonized and deforested the Laguna Las Pozas basin for agriculture while adjacent, abandoned terrain was undergoing reforestation. After discussing the archaeological utility of magnetic analyses, we conclude that following the Maya collapse, some refugee populations migrated to geographically marginal non-degraded landscapes within the southern lowlands not previously occupied by the Classic Maya.