Spring discharge from the Masingini catchment plays a crucial role in the Zanzibar Municipality water supply scheme. However, there has been remarkable attenuation in spring discharge over the years due to a change in rainfall patterns. The study's objective was to assess the effect of rainfall variability on Mtoni and Bububu springs discharge in the Masingini catchment. It analyzed rainfall variability on the Masingini catchment between 1992 and 2018 to assess spring discharge at least ten years before and after the water policy. The monthly rainfall data was collected from Tanzania Meteorological Agency in the Zanzibar office. The spring discharge data was collected from Zanzibar Water Authority and supplemented by field measurements of monthly groundwater levels for wet and dry seasons from fifteen boreholes. The data analysis was carried out using the M-K test. The results revealed a non-significant downward trend in seasonal rainfall over rainfall stations due to the decline of seasonal rainfall over the years. Annual rainfall showed a significant decreasing trend for Kizimbani Agromet station (p < 0.05). On the other hand, the groundwater level dropped by an average of 5±2.6m between the long rainy and dry seasons. The maximum and minimum spring discharges coincide with wet and dry seasons, respectively. There was a significant decreasing trend in annual spring discharge at α = 0.05 and α = 0.01 for Mtoni and Bububu spring discharge, respectively. The M-K revealed a significantly positive correlation of annual spring discharge and rainfall, τ = 0.333 and τ = 0.453 for Mtoni and Bububu spring, respectively, implying that discharge increases as rainfall increases. The average daily discharge of Mtoni and Bububu spring declined by 23.9% and 18.9%, respectively, before and after water policy. The study concluded that rainfall variability was the primary hydroclimate factor for declining spring discharge on the catchment.