As a follow-up to the project “Springs in the Bavarian National Parks as Indicators of Climate Change (SpringNPB)”, a standard methodology for using springs as sentinel environments of climate change was transferred to the UNESCO Rhön Biosphere Reserve and other Bavarian middle-elevation mountain ranges. We studied diatoms from fifteen springs selected in the UNESCO Biosphere Reserve (9) and Steigerwald Nature Park (6). A total of 127 species belonging to 40 genera were found sampling 3 microhabitat types (lithic materials, hygrophilous or aquatic vegetation, and surface sediments). The cumulative percentage of endangered species according to the Red List was 41.5%. These very shaded, low–medium conductivity, low-discharge forest springs are fed by small surficial aquifers. As a consequence, the discharge fluctuates widely, and some springs even occasionally fall dry. Our results could contribute to the use of diatoms as indicators of discharge variability/desiccation in springs: springs affected by discharge variability have lower diatom species richness and distinct diatom communities; diatom indicators and metrics can be validated using invertebrates; larger databases will be necessary to identify the most suitable diatom indicators.