Regional-scale estimates of groundwater recharge are inherently uncertain, but this uncertainty is rarely quantified. Quantifying this uncertainty provides an understanding of the limitations of the estimates, and being able to reduce the uncertainty makes the recharge estimates more useful for water resources management. This paper describes the development of a method to constrain the uncertainty in upscaled recharge estimates using a rejection sampling procedure for baseflow and remotely sensed evapotranspiration data to constrain the lower and upper end of the recharge distribution, respectively. The recharge estimates come from probabilistic chloride mass-balance estimates from 3,575 points upscaled using regression kriging with rainfall, soils and vegetation as covariates. The method is successfully demonstrated for the 570,000-km2 Cambrian Limestone Aquifer in northern Australia. The method developed here is able to reduce the uncertainty in the upscaled chloride mass-balance estimates of recharge by nearly a third using data that are readily available. The difference between the 5th and 95th percentiles of unconstrained recharge across the aquifer was 31 mm/yr (range 5–36 mm/yr) which was reduced to 22 mm/yr for the constrained case (9–31 mm/yr). The spatial distribution of recharge was dominated by the spatial distribution of rainfall but was comparatively reduced in areas with denser vegetation or finer textured soils. Recharge was highest in the north-west in the Daly River catchment with a catchment average of 101 (61–192) mm/yr and lowest in the south-east Georgina River catchment with 6 (4–12) mm/yr.