Precipitation in urine-separating toilets (NoMix toilets), waterless urinals, and conventional urinals causes severe maintenance problems. Additionally, the partial fixation of nutrients in precipitates may affect the later use and treatment of source-separated urine. The goal of this study was to characterise the mineral composition of the precipitates and to identify the main causes for precipitation. X-ray diffraction analysis showed that the main crystalline compounds are struvite, hydroxyapatite, and calcite. We measured concentrations in the solutions of the traps and of the urine collection tank for estimating saturation indices, extent of urea degradation, urine dilution, and elimination of solutes. Our results indicate that bacterial urea degradation triggers precipitation. The composition of the precipitates depends on the urine dilution with flushing water: in low diluted urine, struvite is the main compound, while calcite dominates in systems with high urine dilution. HAP occurs over a wide range of dilution factors. A high fraction of phosphate is incorporated into the precipitates. Dilution with tap water increases this fraction by providing the limiting calcium and magnesium ions. Currently, constructing exchangeable traps seems to be the best solution to deal with problematic precipitation.