The Cotzumalhuapa Nuclear Zone (CNZ) is a Late Classic site consisting of three large architectural compounds linked by a series of stone-paved causeways and bridges. The majority of the site, however, lies beneath layers of recent tephra, leaving the structure of this settlement largely unknown. This study uses ground-penetrating radar (GPR) to map the subsurface near El Baúl, one of the main compounds, in order to examine the spatial relationship among urban architectural features. Excavation within areas of the GPR survey provides fine-grain detail of one major architectural feature in the region, the Gavarrete Causeway. The complimentary nature of these data sets characterizes the architectural organization of the settlement at two scales. Spatial patterning between large-scale architectural features supports the hypothesis that the CNZ represents an integrated urban center with evidence of planned community organization characteristic of other Late Classic period centers across Mesoamerica.