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The assessment of sediment yield from reservoir siltation requires knowledge of the reservoir’s sediment trap efficiency (TE). Widely used approaches for the estimation of the long-term mean TE rely on the ratio of the reservoir’s storage capacity (C) to its catchment size (A) or mean annual inflow (I). These approaches have been developed from a limited number of reservoirs (N40), most of them located in temperate climate regions. Their general applicability to reservoirs receiving highly variable runoff such as in semi-arid areas has been questioned. Here, we examine the effect of ephemeral inflow on the TE of 10 small ( 280x10(3)m(3)), intermittently dry reservoirs located in the Kruger National Park. Fieldwork was conducted to determine the storage capacity of the reservoir basins. The frequency and magnitude of spillage events was simulated with the daily time step Pitman rainfall-runoff model. Different runoff scenarios were established to cope with uncertainties arising from the lack of runoff records and imperfect input data. Scenarios for the relationship between water and sediment discharge were created based on sediment rating curves. Taking into account uncertainties in hydrological modelling, uncertainties of mean TE estimates, calculated from all scenarios (N=9), are moderate, ranging from +/- 6 to +/- 11% at the 95% confidence level. By comparison, estimating TE from the storage capacity to catchment area (C/A) ratio induces high uncertainty (ranges of 35 to 65%), but this uncertainty can be confined (15 to 33%) when the latter approach is combined with hydrological modelling. Established methods relying on the storage capacity to mean annual inflow (C/I) ratio most probably lead to an overestimation of the TE for the investigated reservoirs. The approach presented here may be used instead to estimate the TE of small, intermittently dry reservoirs in semi-arid climate regions. Copyright (c) 2017 John Wiley & Sons, Ltd.