Despite covering only 2–6% of land, wetland ecosystems play an important role at the local and global scale. They provide various ecosystem services (carbon dioxide sequestration, pollution removal, water retention, climate regulation, etc.) as long as they are in good condition. By definition, wetlands are rich in water ecosystems. However, ongoing climate change with an ambiguous balance of rain in a temperate climate zone leads to drought conditions. Such periods interfere with the natural processes occurring on wetlands and restrain the normal functioning of wetland ecosystems. Persisting unfavorable water conditions lead to irreversible changes in wetland habitats. Hence, the monitoring of habitat changes caused by an insufficient amount of water (plant water stress) is necessary. Unfortunately, due to the specific conditions of wetlands, monitoring them by both traditional and remote sensing techniques is challenging, and research on wetland water stress has been insufficient. This paper describes the adaptation of the thermal water stress index, also known as the crop water stress index (CWSI), for wetlands. This index is calculated based on land surface temperature and meteorological parameters (temperature and vapor pressure deficit—VPD). In this study, an unmanned aerial system (UAS) was used to measure land surface temperature. Performance of the CWSI was confirmed by the high correlation with field measurements of a fraction of absorbed photosynthetically active radiation (R = −0.70) and soil moisture (R = −0.62). Comparison of the crop water stress index with meteorological drought indices showed that the first phase of drought (meteorological drought) cannot be detected with this index. This study confirms the potential of using the CWSI as a water stress indicator in wetland ecosystems.
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