Nature-Based solutions (NBS) are the measures supported by natural processes that can adapt to changing climates and generate diverse social, economic, and environmental benefits. Recognising the potential for additional NBS benefits, and quantifying these benefits is essential as it encourages decision-makers to implement and scale-up NBS initiatives. This paper presents findings from a systematic literature review. The review focused on tools and methodologies used for assessing the environmental benefits of implementing NBS. This review provides a detailed compilation of environmental indicators supported by assessment tools. It also includes a catalogue of tools for evaluating environmental benefits, thereby identifying research gaps. Moreover, this research proposes a methodology that uses an ArcGIS (Architecture of Geographic Information Systems) toolbox to identify habitat changes resulting from the implementation of NBS. The methodology translates CORINE (Coordination of Information on the Environment) land cover classes to EUNIS (European Nature Information System) habitat classes. The developed toolbox was applied to two case studies: Denmark (12 NBS) and the Netherlands (3 NBS). The assessment aimed to compare the habitat changes between 2000 and 2018 as two extreme time points for NBS implementation for both case studies. Results indicate that NBS implementation can change habitats leading to an increase in the Red-necked Grebe population in Denmark and a decline in the Black-tailed Godwit population in the Netherlands (two threatened species). The population change highlights the potential positive and potential negative impacts of NBS in their respective cases. These findings suggest Denmark could benefit from lake construction and restoration projects. At the same time, the Netherlands could invest in wetlands and meadows construction and restoration projects to protect the respective species. They could establish designated breeding zones to ensure their population does not decline rapidly.