Background The burden of childhood dental caries amongst Indigenous Australians is higher than that of other Australians. Because of differences in lifestyle and the evolutionary history of the oral microbiota associated risk indicators may differ. Our objective was to evaluate associations between caries increment, salivary biomarkers, and baseline caries status among a rural Indigenous community in Far North Queensland, Australia.MethodsThis study was part of a trial assessing effectiveness and cost-effectiveness of an intervention to prevent dental caries among children. A baseline epidemiological survey and application of topical caries preventive measures was conducted in 2015, followed-up in 2016 and 2017. Saliva flow rate, pH, buffering capacity and bacterial loads were measured. Caries was scored by the International Caries Detection and Assessment system. The outcome was caries increment. Explanatory variables were sex, being in experimental or comparison group, baseline caries status, saliva flowrate and buffering capacity, pH, and salivary loads of mutans streptococci (MS), Lactobacilli (LB), and yeast. Descriptive statistics assessed frequencies, means and percentages. Chi Square tests compared caries incidence in relation to explanatory variables and Generalised Linear Models with negative binomial regression and log-link explored associations between explanatory and outcome variables. ResultsOf children caries free at baseline, significantly fewer had incipient (p=0.01) and advanced (p=0.04) caries after two years. From Univariate analysis, children in the experimental group experienced fewer tooth surfaces with advanced caries (p=0.02) than children in the comparison group. Having caries at baseline (p=0.02) and low salivary flow rates (p <0.001) saw a significant increase in advanced caries after two years. Children with high salivary loads of MS (p=0.03) and LB (p=0.004) experienced more advanced carious surfaces. Multivariable analysis revealed 58% reduction (p=0.001) in advanced caries among children with high salivary flow rates. Caries increment was 61% (p=0.03) more for incipient and 121% (p=0.007) more for advanced caries among children who harboured higher loads of MS. ConclusionAs with other ethnicities, children with low salivary flow rates and those with high loads of MS had higher incipient and advanced caries increments after two years. These risk assessments can facilitate targeted preventive interventions for such communities. Trial registrationAustralian New Zealand Clinical Trials Registry (ANZCTR), No: ACTRN12615000693527; date of registration: 3rd July 2015.