Urine separation is a promising alternative to present-day’s waste water management. It can help to manage our nutrient flows in a sustainable way. Currently, techniques are being developed to recycle and treat source-separated urine. These techniques, however, must consider the spontaneous processes that change the separated urine. The initial cause of changes is the contamination with microorganisms, which can hardly be avoided in urine-collecting systems. The most important transformation processes are microbial urea hydrolysis, mineral precipitation and ammonia volatilisation. Additionally, a variety of microorganisms, including pathogens, may grow in source-separated urine. In this paper we give an overview of the effects that the spontaneous transformation processes may have. We focus on nitrogen, phosphorus, magnesium, calcium, potassium, sulphur, organic substances, pathogens and the buffering capacity. The discussion is based on own research results and literature reviews. This overview will help to develop appropriate technologies for urine recycling.