ImportanceMore than forty million people from certain tropical countries are at risk of developing a non-conventional form of chronic kidney disease (CKD), CKD of multifactorial etiology (CKDmfo). This is also known as CKD of unknown etiology (CKDu). Worldwide, it kills more than 20,000 people annually.FindingsCKDmfo is a chronic tubulointerstitial renal disease caused by groundwater-induced hydroxy- and fluorapatite nano-crystals and nano-tube formation in renal tubules and cortical tissues, in conjunction with chronic intravascular volume depletion, chronic renal anaemia, and ischemia. To manifest this gradually developing renal failure, consuming hard water having, higher concentrations of calcium, phosphates, and fluoride for more than 10 years is necessary. The disease progresses when the kidneys fail to repair or due to ongoing renal tissue damage in the presence of micronutrient deficiency, chronic dehydration, renal ischemia, chronic inflammation, and oxidative stress. These prevents regenerations of renal tissues.ConclusionConsumption of stagnant groundwater concentrated with ions, like Ca2+, PO4, and F− due to prolonged annual droughts over many years, in conjunction with lesser water intake and chronic dehydration, creates a conducive internal milieu for CaPO4 crystallisation in renal tissues. This proposed primary etiology of the crystal-tubular-nephropathy (CTN) provides an insight into a deeper understanding of the use of cost-effective strategies for prevention, early intervention, and eradication of CKD-CTN. In addition to the nano-crystal/nano-tube concept, we provide supporting scientific evidence that Mg2+ in water and the diet does not promote the disease; instead, it prevents crystal formation and developing CKDmfo, as with some other CKDs.RelevanceWe present novel CaPO4 hydroxyapatite crystal formation concepts in a hyperosmolar fluid in renal tissues that causes CKDmfo. Besides, the protective (e.g., magnesium) and enhancing (e.g., dehydration, drinking stagnant hard water) mechanisms that cause CKD-CTN are explored. A new understanding of causative mechanisms paves a path for cost-effective targeted interventions to prevent and eliminate CKDmfo. These principles apply to all CKDmfo/CKDu-affected countries to protect the renal health of farm labourers and others who regularly engage in physical work in hot and dry environments. Providing affordable potable water, increasing water consumption, and avoiding harmful behaviours are critical measures for eliminating CKDmfo.