This paper presents a novel model of an elementary autonomous housing complex called Bio-Morpheme, intended to be an element of a Bio-City's structure. Its novelty manifests from the idea of urban form integration with the form of the water transformation cycle in the building and its immediate surroundings. Key factors include the retention and utilisation of rainwater in the Bio-Morpheme. Another feature of the proposal is the potential to use Bio-Morpheme-like complexes as autonomous units or combine them into larger structures based on integrated water management in typologically diverse city zones. Define the urban and architectural features of a Bio-Morpheme complex allowed using the proposed theoretical model to verify the potential for comprehensive water management featuring the utilisation of rainwater and stormwater harvested from roofs, pavements, bicycle paths, and roads. The study assumed climate and hydrological conditions for Krakow, Poland, predicting the potential for application. The authors observed that a Bio-Morpheme's structure allows for incorporating 41% of the collected runoff into its water supply infrastructure and using this water for domestic purposes when the remaining water can be direct to a surface reservoir. The reservoir provides the Bio-Morpheme's residents with direct contact with a water surface and enhances the microclimate. The Bio-Morpheme model is a solution that allows for rationalizing processes in elementary urban structure cells, which has a beneficial effect on lowering the demand for grid-sourced water and the amount of sewage produced. It also allows for introducing a surface reservoir into an urban interior and guarantees the highest quality of the environment and the health of residents.