Objective The aim of this study was to correlate different combinations of manganese (Mn) and iron (Fe) concentration in drinking water with prevalence of dental caries in both primary and permanent dentition, among school children with similar socio-demographic characteristics. Methods Evros region, in North-Eastern Greece, was divided into four areas, according to combinations of levels of Mn and Fe in drinking water (High Mn-high Fe; High Mn-low Fe; Low Mn-high Fe; Low Mn-low Fe). Children of similar socio-economic background, attending either first or sixth grade (primary or permanent dentition, respectively) of elementary schools, were clinically assessed for caries by three dentists. Caries was defined by the use of dmft/DMFT index. A questionnaire answered by the parents was also analysed. Results 573 children were included. Caries prevalence was high in both age groups (64.2 % with mean dmft 3.3 ± 3.6 in primary and 60.7 % with mean DMFT 2.3 ± 2.5 in permanent dentition, respectively). Residence in a high Mn-low Fe area was associated with a significant OR for caries in both age groups [OR (95 % CIs) for primary and permanent dentition was, respectively, 3.75 (1.68-8.37), p = 0.001 and 3.09 (1.48-6.44), p = 0.003], independently of factors like sugar consumption or brushing frequency. Conclusion Prevalence of caries was high in general, and was associated with the combination of high Mn/low Fe levels in drinking water, independently of various sociodemographic factors.