Abstract. The Moderate Resolution Imaging Spectroradiometer (MODIS) employed by Terra and Aqua satellites provides spatially snow covered data with 500 m and daily temporal resolution. It delivers public domain data in raster format. The main disadvantage of the MODIS sensor is that it is unable to record observations under cloud covered regions. This is why this study focuses on estimating the pixel cover for cloud covered areas where no information is available. Our step to this product involves employing methodology based on six successive steps that estimate the pixel cover using different temporal and spatial information. The study was carried out for the Kokcha River basin located in northeastern part of Afghanistan. Snow coverage in catchments, like Kokcha, is very important where the melt-water from snow dominates the river discharge in vegetation period for irrigation purposes. Since no snow related observations were available from the region, the performance of the proposed methodology was tested using the cloud generated MODIS snow cover data as possible "ground truth" information. The results show successful performances arising from the methods applied, which resulted in all cloud coverage being removed. A validation was carried out for all subsequent steps, to be outlined below, where each step removes progressively more cloud coverage. Steps 2 to 5 (step 1 was not validated) performed very well with an average accuracy of between 90-96%, when applied one after another for the selected valid days in this study. The sixth step was the least accurate at 78%, but it led to the removal of all remaining cloud cover.

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