The extent of surface water has been changing significantly due to climatic change and human activities. However, it is challenging to capture the interannual changes and trends of inland water bodies due to their high seasonal variation and abrupt change. We generated a global annual surface water cover frequency dataset (GLOBMAP SWF) from the MODIS land surface reflectance products to describe the seasonal and interannual dynamics of surface water. Surface water cover frequency (SWF) was proposed as the percentage of the time period when a pixel is covered by water in a year. Instead of determination of the water observations directly, the SWF was estimated indirectly by identifying land observations among annual clear-sky observations to reduce the influence of clouds and variability of water body and surface background characteristics, which helps to improve the applicability of the algorithm for different regions across the globe. Regional analysis demonstrates that our estimation results show reasonable performances on frozen water, saline lake, bright surface and cloud-frequent regions. This dataset can be used to analyze the interannual variation and change trend of highly dynamic inland water body extent with consideration of its seasonal variation. The GLOBMAP SWF dataset is provided in Version 1.0 (https://zenodo.org/record/6462883#.YxC16HZBw2w). Here we provide the number of MOD09A1 (MODIS 8-day composite land surface reflectance) clear-sky snow/ice-free observations (NClear) data as a quality dataset of GLOBMAP SWF product. The clear-sky observation refers to the valid MOD09A1 observation that not covered with clouds and snow/ice. The more available clear-sky observations, the more reliable the estimated SWF. The NClear dataset is provided by 296 1200 km × 1200 km tiles at annual temporal and 500 m spatial resolutions in the sinusoidal projection with Geotiff format for each year during 2000-2020. The file is named as "GLOBMAPClearCount. AYYYY001.hHHvVV.V01.tif", where “YYYY” refers to the year of the file, and “HH” and “VV” explains the number of tiles that are the same with MODIS standard tile. The valid range is 0-46, scale factor is 1.0. The NClear of permanent water (land obervation count of 46), permanent snow/ice and terrain shadows are set to 50.