This study describes a new variety of chalcedony with a unique inhomogeneous bluish green hue, named aquaprase. It was discovered in Africa and is considered to be a valuable addition to the gem trade. A multi-methodological approach was used to examine its chemistry, mineralogy and microstructure, which were then compared to those of chrysoprase and agate, two of the most popular varieties of chalcedony. Optical microscopy revealed a complex microstructural heterogeneity in the different colour intensity areas/bands of aquaprase and agate, whereas chrysoprase exhibited a more homogeneous coexistence of micro- and cryptocrystalline quartz. High-resolution synchrotron XRD was essential for highlighting the complex assemblage of various types of α-quartz in aquaprase and agate (which differ in terms of crystal size and/or cell parameters). Micro-Raman spectroscopy revealed α-quartz and moganite in all three varieties of chalcedony and the presence of the nickel-bearing layered silicate mineral, willemseite, in chrysoprase, which is responsible for its green colouration. The chemical analysis displayed a homogeneous composition of agate, as well as high levels of nickel content in the chrysoprase variety. Aquaprase showed significant amounts (ppm by weight) of trace elements (Al, Mg, Na, K, Ca, Ti, U and Fe) characteristic of its formation environment, as well as high values of Cr, which are thought to be the cause of its bluish green colouration.