Flood protection infrastructures are crucial for enhancing the resilience of societies exposed to natural hazards. Newly designed infrastructures are evaluated for sustainability using a coherent and internationally recognized method defined by the International Hydropower Association (IHA). However, in operation, old structures require a different assessment approach. Different work proposes a modified IHA protocol, mHSAP, which identifies opportunities for improvement and develops a sustainability evaluation framework for existing infrastructures. This paper applies the modified protocol to evaluate the sustainability of two types of flood protection structures: a unique canal system for flood–drought protection of an urban area and a flood protection dike. The time of operation of these structures is over 250 years and over 50 years, respectively. The application of the modified framework demonstrates its advantages in identifying areas for improving flood protection structure operation while maintaining the structure’s sustainability. It also illustrates how Romanian water boards can use such tools to facilitate collaboration between structure owners and stakeholders, allowing them to assess the risks and effects of flooding on society. Through these two examples from Romania, we also show that the mHSAP framework has the potential to actively support the fulfillment of the United Nations Agenda 2030 Sustainable Development Goals (SDGs). The results presented here show that this method can be further utilized by water board authorities to account for climate change effects, address related challenges in a coordinated and efficient manner, develop resilient flood management strategies, inform infrastructure investment decisions, and enhance collaboration among water management authorities.