Salivary biomolecules are considered important modulators of the oral microflora, with a potential subsequent impact on dental health. The present study aimed to investigate the relationship between salivary enzymatic activity and carious experience in children. The carious experience of a sample of 22 school children was evaluated by calculating dmf/DMF indices, following WHO recommendations. Unstimulated whole saliva was collected, and salivary alpha-amylase levels, total protease activity, and matrix metalloproteinase levels (MMP-8 and MMP-9) were measured. The data were analyzed using parametric and nonparametric tests. Our findings revealed no significant relationship between the investigated salivary parameters and the carious experience in permanent teeth (DMFT/DMFS scores). Carious indices scores for primary teeth (dmft and dmfs) were positively associated with MMP-8 levels (r = 0.62, p = 0.004 and rs = 0.61, p = 0.006, respectively) and MMP-9 levels (r = 0.45, p = 0.05 and rs = 0.48, p = 0.039, respectively) and negatively associated with alpha-amylase levels (rs = −0.54, p = 0.017 and rs = −0.59, p = 0.006, respectively). Although with a marginal significance, PEK−054 levels positively correlated with dental caries, while for PFU−089, a negative correlation was observed. These results suggest that salivary alpha-amylase and MMP-8 and MMP-9 levels may be considered potential indicators of carious experience in children. Further studies with a prospective design are needed in order to elucidate the role of these biomolecules in caries development.