Lakes are the most prevalent and predominant water repositories on land surface. A primary objective of the Surface Water and Ocean Topography (SWOT) satellite mission is to monitor the surface water elevation, area, and storage change in Earth’s lakes. To meet this objective, prior information of global lakes, such as locations and benchmark extents, is required to organize SWOT’s KaRIn observations over time for computing lake storage variation. Here, we present the SWOT mission Prior Lake Database (PLD) to fulfill this requirement. This paper emphasizes the development of the “operational PLD”, which consists of (1) a high-resolution mask of ~6 million lakes and reservoirs with a minimum area of 1 ha, and (2) multiple operational auxiliaries to assist the lake mask in generating SWOT’s standard vector lake products. We built the prior lake mask by harmonizing the UCLA Circa-2015 Global Lake Dataset and several state-of-the-art reservoir databases. Operational auxiliaries were produced from multi-theme geospatial data to provide information necessary to embody the PLD function, including lake catchments and influence areas, ice phenology, relationship with SWOT-visible rivers, and spatiotemporal coverage by SWOT overpasses. Globally, over three quarters of the prior lakes are smaller than 10 ha. Nearly 96% of the lakes, constituting over half of the global lake area, are fully observed at least once per orbit cycle. The PLD will be recursively improved during the mission period and serves as a critical framework for organizing, processing, and interpreting SWOT observations over lacustrine environments with fundamental significance to lake system science.