The historic Waterberg platinum deposit, ~15 km WNW of Mookgophong (formerly Naboomspruit), Limpopo Province, South Africa, is a rare fault-bound hydrothermal vein-type quartz-hematite-platinum-group mineralization. As a continuation of the geochemistry and ore mineralogy studies (Part I, Oberthür et al., 2018), this paper concentrates on the ore-bearing quartz and on the age constraints of ore formation. The state-of-the-art methods used include cathodoluminescence microscopy, electron probe microanalysis (EPMA) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) of trace elements, stable isotope (δ18O) analysis and fluid-inclusion studies. U-Pb and (U-Th)/He radiometric age determination gave ages of 900–1075 Ma suggesting platinum-group element (PGE) mineralization as a result of upwelling fluids with connection to the Bushveld complex during Kibaran tectonic movements along the Thabazimbi–Murchison Lineament. Felsic fragments containing Qtz-1 were cemented by different quartz generations (Qtz-2 to Qtz-4) and enable the characterization of the changing physicochemical parameters during multistage mineralization and cooling. The PGE minerals are associated with the earliest hydrothermal stage represented by botryoidal radial-fibrous quartz aggregates (Qtz-2a) which formed on brecciated felsite. The other quartz types are essentially barren. Cathodoluminescence studies of quartz indicate very high Al, Fe and K concentrations as confirmed by EPMA and LA-ICP-MS, whereas Ti is always very low. The varying Al concentrations in the quartz mainly indicate pH fluctuations, the high Fe3+ points at high oxygen fugacity. Micro-inclusions of iron oxide are associated with Pt ore (Fe, Pt, Pd, Au, W, Sb, As), rutile, kaolinite and muscovite. The hydrothermal activity must have been characterized by low saline (<10 wt%) H2O–NaCl solutions. These fluids mixed with original high-saline NaCl ± CaCl2 ± CO2 brines in the brecciated felsite (Qtz-1). According to the quartz-hematite geothermometer the ore depositional temperatures were ~370–330°C (Qtz-2a), whereas the successive quartz veins formed during cooling towards ~295°C. The transport of PGE must have been facilitated by strongly oxidizing chloride complexes of relatively low salinity and moderate acidity.