The Global Lakes and Wetlands Database (GLWD)
Developed by the World Wildlife Fund (WWF) in partnership with the Center for Environmental Systems Research, University of Kassel, Germany. Downloadable at the WWF's website.
- Used by Henderson et al. (2018), to predict where nighttime lights are observed.
SRTM Water Body Data (SWBD)
Created by the National Geospatial-Intelligence Agency (NGA) as a by-product of SRTM elevation data (see this post). The data is available here as thousands of shapefiles, each of which contains 1 by 1 degree area.
Natural and artificial lake polygons can be obtained from the Lakes + Reservoirs data of Natural Earth.
GSHHG (Global Self-consistent, Hierarchical, High-resolution Geography Database)
This database also contains "islands within lakes" and even "ponds within islands within lakes".