Progressing urbanisation is one of the key causes of environmental degradation. This problem also applies to stormwater management. For this reason, drainage infrastructures should be designed in harmony with nature and the decision for selecting a specific stormwater management system solution must not be taken on an ad-hoc or single-perspective basis. The purpose of this paper is to identify the criteria for selecting the best solution for a problem involving the selection of a stormwater management system, and to present a method that will enable all relevant criteria to be taken into account in the decision-making process. The developed decision problem structure takes into account all criteria related to the construction and operation of stormwater infrastructure, and its individual elements were identified based on the analysis and synthesis of information regarding the principles of stormwater management in Poland. The presented approach will allow for the taking into account of all, often mutually exclusive, criteria determining the choice of the stormwater management system option. This, in turn, will make it possible to significantly simplify the decision-making process. The indicated criteria can form the basis for choosing the most favorable stormwater management system for both large urban catchments and individual facilities. Thanks to the considerable flexibility of the developed decision problem structure, its widespread application can contribute to improving the efficiency of stormwater management systems. An example of the developed model’s application in a decision-making process is presented, concerning the selection of a design variant of a single-family residential building’s stormwater management system in Poland. Four design variants were included in the analysis, and the Analytic Hierarchy Process was used as the tool to select the most favorable option. This study shows that nature-based solutions are the most beneficial decision stormwater management options.