With increasing urban expansion and rising global demand for food production, integrating aquaponics within the urban contexts can be considered an alternative sustainable solution to enrich the local production and self-sufficiency. In this research, we aim to study the aquaponics system and provide a design guide for implementing the urban version of the system in the city of Malmo. The design guide will be also practically tested in a form of an architectural proposal at the end of the research. To reach the results, various case studies and academic research were investigated. In addition to other qualitative and quantitative methodologies, such as interviews, questionnaire, and ethnographic studies that contributed to making progress during the research’s different phases. The analysis of data was to generate sustainable bases for urban aquaponics that go in line with the city’s conditions and citizens’ aspirations. Accordingly, several methods and techniques were deducted to be used for the sustainable integration of the aquaponics system within the urban context of Malmo. Nevertheless, the integration process can contribute to including other operations with the aim of increasing aquaponics sustainability and solving urban issues within the context. However, the design guide produced in this paper is mainly for the city of Malmo, but it can be adjusted to other social and geographical contexts.