Water conservation (WC) is an essential terrestrial ecosystem service that mitigates surface runoff and replenishes groundwater, which has received considerable attention under the dual pressures of climate change and human activity. However, there is insufficient understanding of the trends in WC changes on temporal (annual, monthly, daily), spatial, and ecosystem scales. This study proposed a quantitative assessment methodology framework (QAMF) for analyzing the spatiotemporal variation of WC under different discontinuous ecosystems. The QAMF mainly used models and methods such as the hydrological model (SWAT), calibration and uncertainty program (SWAT-CUP), WC calculation formula (water balance method), and spatial analysis method (empirical orthogonal function and wavelet analysis). It was applied to the source region of the Yellow River (SRYR), where the ecological landscape pattern underwent varying degrees of degradation, and WC capacity decreased. The results show that: Firstly, the constructed SWAT in the SRYR had high accuracy, and the proposed formula for calculating WC was suitable for multi-temporal scale analysis of WC in spatially distributed discontinuous basins. Secondly, the annual and monthly WC were respectively 81.00–184.13 mm and −28.58–107.64 mm, and daily WC was positive during extreme precipitation periods and negative during dry periods. The regulating effect of WC was fully reflected on the daily scale, partially reflected on the monthly scale, and absent on the annual scale. Third, the crucial WC area was mainly distributed in the southeast, and there was a significant primary yearly cycle of WC in the SRYR. Finally, different ecosystems exhibited different WC capabilities, and protecting the diversity of ecosystems played an essential role in maintaining and improving the WC function in the SRYR. This project has great scientific significance and technological support for scientifically evaluating the WC capacity in the SRYR.
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