This article presents a comprehensive subpixel water mapping algorithm to automatically produce routinely open water fraction maps in the Tibetan Plateau (TP) with the Moderate Resolution Imaging Spectroradiometer (MODIS). A multi-index threshold endmember extraction method was applied to select the endmembers from MODIS images. To incorporate endmember variability, an endmember selection strategy, called the combined use of typical and neighboring endmembers, was adopted in multiple endmember spectral mixture analysis (MESMA), which can assure a robust subpixel water fractions estimation. The accuracy of the algorithm was assessed at both the local scale and regional scale. At the local scale, a comparison using the eight pairs of MODIS/Landsat 8 Operational Land Imager (OLI) water maps demonstrated that subpixels water fractions were well retrieved with a root mean square error (RMSE) of 7.86% and determination coefficient (R²) of 0.98. At the regional scale, the MODIS water fraction map in October 2014 matches well with the TP lake data set and the Global Lake and Wetland Database (GLWD) in both latitudinal and longitudinal distribution. The lake area estimation is more consistent with the reference TP lake data set (difference of −3.15%) than the MODIS Land Water Mask (MOD44W) (difference of −6.39%).

Based on a linear spectral mixture model and multiple endmember spectral mixture analysis, using daily advanced very-high-resolution radiometer (AVHRR/2) data of the Qinghai–Tibet Plateau, a subpixel snow mapping algorithm was proposed in this paper, for prolonging the historical time series of the fractional snow cover data to 40 years. In particular, the normalized difference vegetation index (NDVI), and channels 1 and 2 of AVHRR/2 data were used to automatically select the end-members directly, from a certain AVHRR/2 image. A look-up table of sample spectra of mixed pixels and their respective snow cover percentages was introduced for one AVHRR/2 image. According to the established look-up tables, the fractional snow cover of each mixed pixel can then be extracted from the AVHRR/2 images. Before the subpixel snow mapping, the cloud pollution of the AVHRR/2 images was mitigated, with both the thick and thin clouds almost removed from the AVHRR/2 images. It turns out that the processing speed of the subpixel snow mapping is three times faster than the process not using the look-up table. The mapping algorithm was validated against the snow-covered area from Thematic Mapper (TM) data, with the root-mean-square errors (RMSEs) well below 0.12. Results show that the proposed algorithm for subpixel snow mapping is both effective and efficient, especially in such a mountainous region as the Qinghai–Tibet Plateau.