The Provincial Government of East Nusa Tenggara of Eastern Indonesia has intended to construct a new regional landfill site in Pitay–Kupang, which would accommodate municipal waste of two cities. Considering that environmental degradation in landfill sites has been a substantial issue for many developing cities in Indonesia, this study evaluates the pre-determined site on a local scale based on environmental geology parameters. It employs a conventional Geographical Information System based—Multi-Criteria Decision Analysis (GIS-MCDA) method which is based on the analysis of regional criterion, assessed by expressing values on each parameter presented on thematic maps and overlaid altogether as a screening process, and the exclusion criterion analysis, which sets a buffer zone to filter out irrelevant locations. The regional criterion parameters are: Lithology, groundwater depth, slope gradient and rainfall intensity, whilst the exclusion criterion parameters are: Distance from rivers and lakes, shorelines, settlements, main roads, airports and protected areas, distance from potential geological hazards such as fault zones, floods and mass movements, and distance from any geological potential which may be developed in the future. The biggest area reduction for suitable landfill site candidate is lithology, correlating with groundwater depths, and distance from rivers. Here we identified four potential sites located west and centre of Pitay, situated on Bobonaro scaly clay lithology unit, arguably possessing no groundwater with a slope gradient of 0–20%, rainfall intensity below 1000 mm, and is distant from any potential hazards, promising geological resources and other unfavorable criteria relating to environmental degradation.