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Despite the widespread presence of groundwater recharge check dams, there are few studies that quantify their functionality. The objectives of this study are (i) to assess groundwater recharge in an ephemeral river with and without a check dam and (ii) to assess sediment build-up in the check-dam reservoir. Field campaigns were carried out to measure water flow, water depth, and check-dam topography to establish water volume, evaporation, outflow, and recharge relations, as well as sediment build-up. To quantify the groundwater recharge, a water-balance approach was applied at two locations: at the check dam reservoir area and at an 11 km long natural stretch of the river upstream. Prediction intervals were computed to assess the uncertainties of the results. During the four years of operation, the check dam (storage capacity of 25,000 m³) recharged the aquifer with an average of 3.1 million m³ of the 10.4 million m³ year⁻¹ of streamflow (30%). The lower and upper uncertainty limits of the check dam recharge were 0.1 and 9.6 million m³ year⁻¹, respectively. Recharge from the upstream stretch was 1.5 million m³ year⁻¹. These results indicate that check dams are valuable structures for increasing groundwater resources in semi-arid regions.