Abstract Assessing the combined impacts of future climate and socio-economic change at the country level is vital for supporting national adaptation policies. Here, we use a novel modelling approach to study the systemic impacts of climate and socio-economic changes on the Czech Republic, taking account of cross-sectoral interactions between agriculture, water, forestry, land-use and biodiversity, and, for the first time, trans-national interactions. We evaluate the national-level baseline results, scenario-neutral model sensitivities, and climate and socio-economic scenario impacts using a European-scale integrated modelling tool. Consistently across most climate and socio-economic scenarios, the Czech Republic is projected to have increasing importance as a crop-growing region in Europe, due to an increased competitive advantage within the continent. Arable land in the Czech Republic expands, at the expense of livestock farming and forestry, with associated impacts of increased water scarcity and reduced biodiversity for the country. Accounting for trans-national interactions in national-scale assessments provides more realistic assessments of impacts and helps to identify the changing role of the country within its regional and continental domain. Such improved understanding can support policy-makers in developing national adaptation actions that reduce adverse impacts and realise opportunities.