Activities performed over long periods of time tend to leave soil chemical residues as evidence of those activities. Some of the questions studied in this paper deal with the interpretive capabilities provided by chemical patterns. Soil samples from Cerén, El Salvador, a well-preserved site, were analyzed for extractable phosphorus and heavy metals. We compared in situ artifacts collected from the site with chemical signatures that indicate activity areas. We found that elevated concentrations of phosphorus were associated with food preparation, consumption, and disposal. Heavy metals were associated with the interior of the structure where pigments and painted gourds were found. In this case, where well-preserved, in situ artifacts were available for analysis, we found that chemical analysis was effective in locating human activity areas. Our findings indicate that chemical analysis can be used to guide interpretation in areas of poor artifact preservation with reasonable accuracy, and in archaeological sites that underwent gradual abandonment.