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The paper presents the use of indicators in a site-specific assessment method for strategic environmental assessment in regional land use planning (here: SEA-REP). It is explained with the example of the state of environment indicator ‘LUCCA 4—Urban Areas at Risk of Flooding’, how SEA as a decision-aiding instrument can contribute to the prevention of conflicts with policy for adaptation to climate change. The method begins with the determination of impact factors for SEA. In the presented study, the physical impact factors of land consumption, land use change, and directed flooding were recognised. A core problem during the selection of indicators for land uses for the adaptation to climate change (here: LUCCA) and the derivation of assessment thresholds was a lack of region-wide policy objectives for the protection of land and resources. Therefore, in a second step, regional environmental orientation objectives were derived from national and EU environmental policy. A standard method for the selection of LUCCA indicators and the derivation of assessment thresholds for conflict analysis is described. Three classes of conflict classification for regional plan designations on the individual site are proposed. It is recommended that future adaptation measures of regional land use planning should be designations of specific land uses as priority areas for urban areas prone to flood risk.