Valuable and rare materials in seawater brine are often discarded during desalination. However, there is an increasing focus on recovering these resources, rather than minimizing their disposal volume, due to the economic and environmental opportunities it can bring. Despite this shift, current Sustainability Assessment (SA) studies in desalination tend to overlook the brine handling and social dimensions, and brine treatment assessments remain predominantly centered on techno-economic dimensions. Therefore, in this work, we propose a comprehensive and transparent framework for the sustainability assessment of integrated desalination and resource recovery options. The framework not only evaluates pre-defined systems but supports the identification of system features of interest, such as products to assess and technologies to include, as well as the transparent selection of indicators when considering specific contexts. To develop this framework, a critical review of the literature on SA in desalination and brine treatment systems was conducted. Looking at the identified gaps, we synthesized the findings and key messages and proposed the integration of Multi-Criteria Analysis and Value-Sensitive Design in the decision-making process. This allows stakeholders to be involved and incorporates their values at different stages of the assessment, making it distinct from traditional SA methods. This framework offers structured guidance to stakeholders on how to carry out qualitative and quantitative assessments while ensuring transparency in the assessment process. This work serves as a foundational contribution to benefit future research on the development of a sustainable desalination industry, valuing the input and involvement of all stakeholders.