As part of an IUCN-led project, this document outlines optimal solutions for a critical sites network that best represents freshwater biodiversity in the Lake Victoria Basin (LVB). Using this approach the authors provide a foundation for species conservation through site protection whilst also maximising species climate resilience and sustainable livelihoods. They employ: (1) an updated assessment of species threatened status (IUCN Red List status); (2)a preliminary network of freshwater Key Biodiversity Areas (KBAs); (3) an assessment of species livelihoods values; and (4) an evaluation of species climate vulnerability to investigate options for a critical sites network that better represents freshwater biodiversity than the current protected areas networks. The systematic conservation planning software Marxan is employed to identify optimal site networks meeting a range of pre-set targets. This document highlights, within the LVB, potential networks of freshwater sites that best meet targets for the inclusion of threatened species, freshwater KBAs, climate vulnerable species and species of high value to livelihoods. The proposed site networks will form the basis of advice for protected areas managers in the LVB countries such that the current Protected Areas networks might be modified, expanded or managed to better represent the conservation needs of freshwater biodiversity.