Sediment control is important for supplying clean water. Although check dams control sediment yield, site selection for check dams based on the sediment trapping efficiency (TE) is often complex and time-consuming. Currently, a multi-step trial-and-error process is used to find the optimal sediment TE for check dam construction, which limits this approach in practice. To cope with this challenge, we developed a user-friendly, cost- and time-efficient geographic information system (GIS)-based tool, the trap efficiency tool (TET), in the Python programming language. We applied the tool to two watersheds, the Hableh-Rud and the Poldokhtar, in Iran. To identify suitable sites for check dams, four scenarios (S1: TE ≥ 60%, S2: TE ≥ 70%, S3: TE ≥ 80%, S4: TE ≥ 90%) were tested. TET identified 189, 117, 96, and 77 suitable sites for building check dams in S1, S2, S3, and S4, respectively, in the Hableh-Rud watershed, and 346, 204, 156, and 60 sites in S1, S2, S3, and S4, respectively, in the Poldokhtar watershed. Evaluation of 136 existing check dams in the Hableh-Rud watershed indicated that only 10% and 5% were well-located and these were in the TE classes of 80–90% and ≥90%, respectively. In the Poldokhtar watershed, only 11% and 8% of the 207 existing check dams fell into TE classes 80–90% and ≥90%, respectively. Thus, the conventional approach for locating suitable sites at which check dams should be constructed is not effective at reaching suitable sediment control efficiency. Importantly, TET provides valuable insights for site selection of check dams and can help decision makers avoid monetary losses incurred by inefficient check-dam performance.