: Pre-industrial emission levels can serve as a basis to set emission requirements in current conditions to approximate natural circulation of resources and protect the environment. In Denmark, the year 1900 has been set as a reference for water regulation purposes. Reliable measurements from this time are not available. To define reference conditions, we estimate point source emissions of nutrients from Danish towns in 1900 based on historic documentation and current quantitative data. The flow of nutrients emitted by humans and animals and in industrial wastewater is quantified based on the assessment of typical discharge routes in a set of model towns. We find that point source emissions were significant, with 4261 t nitrogen and 764 t phosphorous emitted from towns in 1900. The main source were human excrements (61%), followed by excrements of animals held in towns (32%) and industry (6%). 59% of nutrients was discharged directly to water, 22% were used as fertilizer on agricultural soil and 19% was emitted to soil via landfills and spills. Current point source emissions of nutrients to water (6,600 tN/yr) are significantly higher than our results, revealing a need for radical reductions if historic emission levels should not be exceeded in the future.