Various types of small-scale wastewater treatment systems are widely used in rural areas, and life-cycle assessment (LCA) should be performed to evaluate their environmental performance. In this study, septic systems were first classified into five categories based on their wastewater treatment performance. Effluent samples from actual systems were collected, and their water qualities were determined. A model to evaluate the environmental load from the septic systems using LCA methods was then established. The water-quality values obtained were input to the model, and the life-cycle environmental costs of the classified septic systems were calculated. The mean environmental load of the effluent during the operation stage was 37.6%, confirming that evaluation of an effluent discharge inventory using LCA, inspection, and water-quality monitoring to improve operations is critical for reducing the environmental load. The operation stage accounts for over 99% of the involved eutrophication, biological toxicity, and toxic chemicals, which are strongly related to the quality of the effluent. Evaluation of the effluent discharge inventory using LCA is of great significance, even for small-scale wastewater treatment systems. The set of procedures developed in this study can be used to calculate comprehensive environmental impacts at wastewater treatment plants.