The formation of ephemeral gullies in agricultural fields has been recognized as an important source of sediment contributing to environmental degradation and compromising crop productivity. Methodologies are being developed for assessing gully formation and gully sediment yield. The Annualized Agricultural Non-Point Source (AnnAGNPS) pollution model is an important tool for multi-temporal watershed-scale simulations because it contains the necessary components for ephemeral gully investigation, making AnnAGNPS a commonly used tool for evaluations of agricultural conservation and operation practices. AnnAGNPS requires the user to define the location of ephemeral gullies throughout the watershed, what often constitutes a time consuming task where users may not accurately locate and describe all ephemeral gully locations. Alternatively, herein a GIS-based graphical user interface is described for the automated identification of areas with high probability of forming ephemeral gullies, referred to as potential ephemeral gullies (PEGs), based on the modified Compound Topographic Index (CTI). Through the aid of a study case, PEG mouth locations along with their attributes are generated through an iterative procedure by varying different CTI threshold values (99.9%, 99.5%, 99.0%, 98.5%, and 98%). Three sets of yielded PEG mouth locations and corresponding attributes were then integrated with AnnAGNPS for assessment of the impact of potential ephemeral gullies in the watershed sediment erosion. Analysis of the spatial distribution of estimates of annual average of gully erosion identifies the sub-watersheds prone to ephemeral gully erosion, thus enhancing the applicability of AnnAGNPS to evaluate conservation practices and/or targeted interventions designed to address ephemeral gully erosion at the watershed-scale.