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This investigation focuses on the transformation of the settlement pattern of a lowland landscape as a social response to the hydrological challenges emerging in the late 13th century (c.) overture of the Little Ice Age (LIA). Results of the applied zonal analysis suggested a strong spatial connection between the geomorphological conditions, the agro-ecological suitability (good-excellent, medium and low) and the stability or instability of settlement patterns. The elevation means of archaeological sites in the deserted zones proved significantly lower than those in zones with permanent settlement pattern (BrunnerMunzel test p <= 0.01; n = 377). Additionally, the late medieval (14th-mid-16th centuries) site group was situated, on average, significantly higher than the high medieval (late 10th-13th centuries) site group within the permanent zones (Brunner-Munzel test p <= 0.01; n = 219). These outcomes statistically confirm that not only did low-lying inhabited areas shrink significantly, but they also displaced vertically in the first phase of the LIA. When analysing the relation of settlement pattern to soil conditions, the proportion of areas with good-excellent agro-ecological suitability proved 1.5-2 times higher in the permanent zones than in the deserted and uninhabited settlement suitability zones. Using the linear model, different regression coefficients appeared between the extension of the high and medium agroecological suitability zones and the number of high and late medieval settlements. The different coefficients in the studied two periods suggest that the issue of agroecological suitability in the High Middle Ages did not bear such importance as in the late Middle Ages. The findings of the paper may contribute to answering the question why the relatively dense settlement pattern of the deserted zones was abandoned almost completely by the end of the 13th c. in areas where flood proneness and weak agro-ecological suitability both meant a serious risk for human communities. Finally, we presumed that if hydro-climatic changes increased water levels, they must have changed the plant composition of the studied landscape as well. Chi-squared test of macrofossil plant remains (narchaeological site = 55; ntaxon =-330) shows that the second part of the 13th c. saw the ratio of species from humid habitat types grow (X-2 = 7.81; df = 1; p = 0.02). Comparison of the two studied processes indicates a broad synchronism between the shrinkage of inhabited areas and the increasing proportion of plants with humid environment tolerance during the second part of the 13th c. The reconstructed transformations in the composition of plant remains and settlement structure signal not a mere transitional change, but a ’longue duree’ structural transformation of the landscape. (C) 2016 Elsevier Ltd. All rights reserved.