Vertical integration, which creates strategic linkages between national and sub-national levels, is being promoted as important for climate change adaptation. Decentralisation, which transfers authority and responsibility to lower levels of organisation, serves a similar purpose and has been in place for a number of decades. Based on four case studies in semi-arid regions in Africa and India, this paper argues that vertical integration for climate change adaptation should reflect on lessons from decentralisation related to governing natural resources, particularly in the water sector. The paper focuses on participation and flexibility, two central components of climate change adaptation, and considers how decentralisation has enhanced or undermined these. The findings suggest that vertical integration for adaptation will be strengthened if a number of lessons are considered, namely (i) actively seek equitable representation from marginal and diverse local groups drawing on both formal and informal participation structures, (ii) assess and address capacity deficits that undermine flexibility and adaptive responses, especially within lower levels of government, and (iii) use hybrid modes of governance that include government, intermediaries and diverse local actors through both formal and informal institutions to improve bottom-up engagement.