This research aims to evaluate the operational effectiveness of current flood protection infrastructure and measures in a flood-prone area using geo-referenced information systems and SWOT analysis. To achieve this, all existing flood protection measures and works in the case study basin, namely Strymonas River basin in Greece, were mapped and recorded. These data, along with water-related spatial information, were stored in a geo-referenced database created within an open-source GIS environment. Additionally, the system was populated with the basin’s recorded historic floods, derived from the European Union’s Floods Directive implementation process. The outputs of the research, which include a spatial comparison of flood protection measures and works with flood event occurrences as well as analyses of the figures, density, and locations of flood protection works, were evaluated as an integrated system and further processed using SWOT analysis. The latter was informed by questionnaire results, and the identified strengths and weaknesses of the flood protection infrastructure were used to explore potential opportunities and threats, which could respectively reinforce or jeopardize the basin’s capacity to effectively respond to future floods. The research framework can be applied to any river basin and could provide important assets in flood protection planning at a basin scale.