The goal of this study is the identification of ecological advantages and disadvantages of alternative sanitation systems in comparison to conventional wastewater treatment. The methodology of Life Cycle Assessment (LCA) is adopted as an evaluation tool for the ecological assessment of various sanitation scenarios for a hypothetical middle-sized settlement in Germany (ca 5000 inhabitants). The scenarios include a reference system with conventional drainage and treatment in an activated sludge plant with anaerobic sludge digestion and sewage gas production. In the alternative scenarios, urine is source-separated in the toilet, collected and applied as fertilizer. Faeces are either collected by gravity drainage and composted together with biowaste or collected by a vacuum system and co-digested with biowaste to gain biogas for energy production. The remaining greywater is treated in a soil filter or in a technical plant (Sequencing batch reactor). All relevant processes of the investigated scenarios are modelled in detail for the Life Cycle Inventory, based on data from pilot plants and literature. This implies the processing of the different waste fractions, transport and energy supply, mineral fertilizer substitution, and sludge incineration. Beside the operational expenditures, the construction phase is included with material and energy demands. The resulting substance flow model is evaluated with a set of environmental indicators relating to the demand of energy, non-renewable resources, climate change, eutrophication, acidification, and various toxicity potentials. As a result, the alternative scenarios cause less environmental burden in almost all impact categories. The source-separation of human excreta disburdens the wastewater treatment process and lowers nutrient emissions into surface waters. The secondary fertilizer from urine and faeces has lower heavy metal content than an average mineral fertilizer. Depending on the system configuration, alternative sanitation systems can have a lower demand for fossil fuels and subsequently cause fewer emissions of climate-active gases. Only the increased emission of acidifying gases represents a considerable drawback compared to the conventional system. A normalisation of all indicators to the average environmental burden of a single person in Germany reveals that the decisive categories for the overall comparison are related to eutrophication, acidification, and terrestrial ecotoxicity. Energy-related indicators have a smaller contribution, but they can be important in terms of world-wide scarce fossil resources and climate change. The advantages of alternative sanitation systems can only be realized if the secondary functions of mineral fertilizer substitution and energy supply are fully utilized. Important key parameters for future LCA studies of alternative sanitation systems are identified, which may simplify the data acquisition. The construction phase has only a minor relevance for the ecological assessment and may therefore be neglected in future studies. In all, the data quality of this LCA study can be further improved, because many processes of alternative systems have not yet been investigated or realized in full-scale. Hence, the development of a universal decision support method could not be realized in a reasonable way due to the lack of adequate long-term process data and the high influence of case-specific boundary conditions on the technical implementation. However, this LCA study gives a first assessment of potential ecological benefits and drawbacks of alternative sanitation systems.