The mobilization and transport of Na+ across the plasma membrane is central to biology. While the sweeping consequences of aberrant extracellular or cytosolic Na+ levels on organism physiology are known, and indeed mapped, at the tissue and single cell levels, sub-cellular Na+ remains unmapped due to a lack of tools of sub-cellular imaging. Here we describe RatiNa, a pH-independent, ratiometric fluorescent reporter for Na+. With RatiNa we successfully imaged organellar Na+ in mammalian cells and C. elegans. Several crucial findings ensue from organelle Na+ measurement: For one, average Na+ levels in endocytic organelles exceeds cytosolic levels but can vary from one vesicle to another. In addition, unlike any other ion mapped so far, lumenal Na+ decreases as endosomes mature. Finally, a drastic change in Na+ levels occur in lysosomes when nematodes adapt to salinity. We found NHX-5, a putative lysosomal Na+/H+ exchanger, is vital for salt adaptation. Since lysosomes play a key role in metazoan metabolism, The ability to image sub-cellular Na+ in vivo may lead to a deeper understanding of Na+ transport and metabolism.