<p>Dental caries is a major public health concern among children, with Streptococcus species, particularly Streptococcus mutans, playing a key role in its development. This study aimed to compare the effect of alkaline water, chlorhexidine mouthwash, and tap water on the salivary Streptococcus count in children aged 10–12 years. A single-blinded preliminary clinical study was conducted on 60 healthy children aged 10–12 years. Three groups of participants were randomly assigned: one group used alkaline water, another group used mouthwash containing 0.12% chlorhexidine, and the third group used tap water as a control. Participants were followed for three weeks. Children with systemic diseases, orthodontic appliances, or recent use of antibiotics or corticosteroids were excluded. Unstimulated saliva samples were collected at baseline and after the intervention. Salivary Streptococcus counts were determined using standard microbiological techniques. After 3 weeks, mean salivary Streptococcus mutans counts (CFU ×10⁵/ml) were 3.0 ± 0.36 in the alkaline water group, 2.1 ± 1.9 in the chlorhexidine group, and 7.9 ± 0.3 in the tap water group. Both intervention groups demonstrated significantly lower bacterial counts compared with the control group (<i>p</i> &lt; 0.001), while chlorhexidine showed significantly lower counts than alkaline water. Within the short-term limitations of this study, rinsing with alkaline water demonstrated a significant reduction in salivary Streptococcus mutans counts, although chlorhexidine showed lower bacterial counts after 3 weeks under the conditions of this study. These preliminary findings suggest its potential as an adjunctive oral hygiene agent, and highlight the need for long-term clinical trials to assess its effectiveness in caries prevention.</p><p><b>Trial registration</b>: The trial was registered with the Clinical Trial.gov (Number and date NCT06511336, 07/09/2024).</p>