To be effective, cross-cutting issues like climate change adaptation need to be mainstreamed across multiple sectors and for this greater policy coherence is essential. Using the cases of Malawi, Tanzania and Zambia, this paper investigates the extent of coherence in national policies across water and agriculture sectors and their links to climate change adaptation and national development plans. A two-pronged qualitative approach is applied using Qualitative Document Analysis of relevant policies and plans, combined with expert interviews from key non-government actors in each country. Findings show that sector policies have differing degrees of cross-thematic coherence, currently being strongest in Zambia and weakest in Tanzania.