Otolith geochemistry is used increasingly as a natural tag to retrospectively determine habitat use in marine fishes. It is necessary to first conduct a thorough assessment of spatio-temporal variability before attempting to use the approach to determine estuarine residency or natal origins. In particular, knowledge of temporal variation at different scales is important when such variability may confound spatial discrimination. We assayed elements and calculated the elemental ratios to Ca (Li:Ca, Mg:Ca, Mn:Ca, Cu:Ca, Sr:Ca, Ba:Ca, Pb:Ca) in otoliths of juvenile Solea solea and Solea senegalensis, collected over several months in 2006 and 2009 in Portuguese estuaries, using laser ablation inductively coupled plasma mass spectrometry (LA ICP-MS). The elemental compositions of the otoliths varied significantly between and within years in both of the species, although the within-year variability did not interfere in spatial discrimination. The overall classification accuracy of juveniles to their estuaries of origin varied among the years and species, ranging from 71.0% to 80.1%. Established elemental signatures constitute the baseline data for future assessments of connectivity between juvenile and adult populations of the two sole species.