It is extremely challenging to quantitate lumenal Ca in acidic Ca stores of the cell because all Ca indicators are pH sensitive, and Ca transport is coupled to pH in acidic organelles. We have developed a fluorescent DNA-based reporter, CalipHluor, that is targetable to specific organelles. By ratiometrically reporting lumenal pH and Ca simultaneously, CalipHluor functions as a pH-correctable Ca reporter. By targeting CalipHluor to the endolysosomal pathway, we mapped lumenal Ca changes during endosomal maturation and found a surge in lumenal Ca specifically in lysosomes. Using lysosomal proteomics and genetic analysis, we found that catp-6, a Caenorhabditis elegans homolog of ATP13A2, was responsible for lysosomal Ca accumulation-an example of a lysosome-specific Ca importer in animals. By enabling the facile quantification of compartmentalized Ca , CalipHluor can expand the understanding of subcellular Ca importers.