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Urban flooding problem has been exacerbated in recent times, especially in developing nations, due to haphazard changes in land use and land cover (LULC) resulting from rapid urban expansion, coupled with river encroachments and inadequately engineered river management structures. Kathmandu Valley Watershed (KVW), encompassing Kathmandu, Bhaktapur and Lalitur districts, the fastest growing cities in South Asia, is constantly growing, with a significant increase in urban areas. Due to urbanization, the watershed’s water storage capacity is diminishing, while surface runoff volume and rate are accelerating. We evaluated the isolated as well as the integrated impact of multiple scenarios of LULC change and river encroachment on flood inundation characteristics in KVW. LULC prediction revealed an increase in built-up areas by 113% between 1990 and 2020, which are further projected to increase by 29% by 2050. Inundation modeling using Rainfall-Runoff Inundation (RRI) model showed that rather than the increase in inundation extent, the depth of inundation is projected to increase in future as a result of increasing urban areas. Furthermore, our research highlighted that the impact of river width encroachment had a more substantial effect on flooding compared to changes in LULC alone. Similarly, integrated impact of LULC change and river encroachment was more pronounced than the impact of change in LULC alone. The aggregate of observations leads to the conclusion that the encroachment of rivers is the predominant factor contributing to the flooding issue within the KVW. The findings of the study is anticipated to assist policymakers in effective land use planning and in proposing appropriate development initiatives concerning the river environment.