Climate change is a topical issue in water management in Africa, because of the complex challenges it confronts institutional actors with in order to respond to these threats. The research undertook an institutional analysis to understand capacities for collaboration, adaptation and precaution in development of water supply systems. Four coastal villages in Ghana were selected as case studies to assess the capacities of institutions to respond and how these deal with existing and future climate change induced sea level rise conditions. The findings show local perceptions are consistent with available evidence of current water salinization vulnerabilities in the area due to rapid coastal erosion and inundation. However, sea level rise will exacerbate the existing problems by causing more frequent storm surges and extension of tidal regimes further inland. It is concluded that: (i) There is a commitment to adaptation but no clear intent of precaution. Local and district institutions adopt incremental (traditional) responses because they lack the requisite capacities to adapt to the scale and complexity involved. Non-traditional externally initiated (International and national institutions) large scale projects have potentials to ameliorate future impacts. However, they are mainly adaptive by intent with precaution only implicit by default of the scale of these developments. (ii) The governance structure presents perplexing constraints and opportunities for institutional collaboration for adaptation action. It is top down, characterized by weak internal capacities, asymmetrical power distribution and poorly coordinated. This undermines collaboration and facilitation of adaptive capacities. Conversely, it shows some robustness and redundancy being multi-layered where collaboration, especially with foreign agencies, provides opportunities for large scale interventions. (iii) Long term adaptation would require certain socio-ecological restructuring, along with a comprehensive and practical climate change adaptation strategy at all scales, where the precautionary principle is integral.