Municipal water systems in Rwanda face challenges such as inadequate infrastructure, population growth, and financial constraints. A multilevel regression model will be employed to analyse data from various municipalities, accounting for both within-municipality variation and municipality differences. The multilevel analysis revealed that an increase in municipal investment by 10% was associated with a 7.5% reduction in waterborne diseases across Rwanda's municipalities (95% CI: 3.2%, 11.8%). This study provides evidence for the effectiveness of targeted investments in reducing health risks from waterborne diseases. Investments should be prioritised in areas with lower municipal investment to maximise risk reduction, and regular monitoring is recommended to ensure sustainability. Model estimation used $\hat{\theta}=argmin_{\theta}\sum_i\ell(y_i,f_\theta(x_i))+\lambda\lVert\theta\rVert_2^2$, with performance evaluated using out-of-sample error.