Surface water plays a vital role in the spread of infectious diseases. Information on the spatial and temporal dynamics of surface water availability is thus critical to understanding, monitoring and forecasting disease outbreaks. Before the launch of Sentinel-1 Synthetic Aperture Radar (SAR) missions, surface water availability has been captured at various spatial scales through approaches based on optical remote sensing data. A critical drawback of the latter is data loss due to cloud cover, however few studies have quantified this. This study evaluated data loss due to clouds in three Western Ghats (India) districts. These forest-agricultural mosaic landscapes, where water-related diseases are prevalent, experience the Indian monsoon. We compared surface water areas mapped by thresholding 10m Sentinel-1A SAR data with the optical 30m Landsat-derived Joint Research Centre (JRC) Global Surface Water product, currently the only globally available long-term monthly surface water data product. Backscatter thresholds were identified manually, and our Bayesian algorithm found these thresholds were very likely (>97%). While the Sentinel-1 SAR-based and JRC’s optical-based approach mapped surface water extent with high overall accuracy (> 98%) when the cloud cover was low, the unmapped surface water area was substantial in the JRC product during the monsoon months. Across the districts, the average cloud cover in the July August period was 92% or 90% for 2017 and 2018 respectively, resulting in 25% or 23% of the surface water area being unmapped. Also, the more detailed 10m resolution of Sentinel-1A SAR helped detect the many small water features missed by 30m JRC. Thus, for predicting water-related disease risks linked to small water features or monsoon rainfall, Sentinel-1A SAR is more effective. Finally, automatic backscatter thresholding for unvegetated surface water mapping can be effective if threshold values are dapted to regional-specific backscatter spatial and temporal variations.