Microbial biofilm communities are composed of fungi, bacteria, and phytoplankton taxonomic groups (e.g., cyanobacteria, diatoms, and chlorophytes), which inhabit the surface of intertidal mudflats. Such biofilms have critical roles in shorebird diets, mudflat stabilization, primary productivity, and carbon storage. These raster datasets represent the presence, nutritional quality, quantity, pigment characteristics, and likely taxonomic groups of biofilms located on the mudflats of South San Francisco Bay in Spring 2021, during peak shorebird migration. To produce these datasets, we used a multi-scalar remote sensing approach that coupled in-situ data coupled with data from an ASD field spectrometer, a HySpex VNIR/SWIR imaging spectrometer (5 mm), and the AVIRIS-Next Generation (NG) airborne imaging spectrometer (3.7 m). Using a suite of modeling approaches, we used these data to develop and scale algorithms of each parameter to the South Bay using an AVIRIS-NG image collected on April 15, 2021. See child items for more information. Maps created using hyperspectral remote sensing data will support managers’ need to visualize shorebird habitat quality and research on drivers of biofilm quality and quantity.