To understand the geological origins of minerals in cryoconite and the nutrients sources for microbes on glaciers, we analyzed the Sr–Nd isotopic ratios of the four mineral fractions in cryoconites including saline, carbonate, phosphate, silicate and the organic fraction obtained from Gulkana Glacier in Alaska. The isotopes in the silicate mineral fraction exhibited spatial variation within the glacier (87Sr/86Sr: 0.704533–0.709563, εNd (0): −16.0 to 0.5), which can be explained by the different mixing ratios of the two distinct sources: one of the sources is lateral and terminal moraines or soil, and the other is the medial moraine of the glacier. The minerals in the cryoconite at the lower sites in the glacier are likely derived from the former source, whereas those at the upper sites are from latter sources. The mineralogical and elemental compositions also support mixing of the silicate minerals from the two local sources. The Sr isotopic ratios of the organic fraction also showed spatial variation on the glacier in the middle sites – a trend similar to those of the phosphate fraction. The results suggest that the organic matter is mostly the byproducts of microbes using the phosphate minerals as a nutrient source.