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The formation of ordered particle arrays plays an essential role in nanotechnology, biological systems, and inorganic photonic structures in the geosphere. Here, we show how ordered arrays of amorphous silica spheres form in deeply weathered lithologies of the Great Artesian Basin (central Australia). Our multi-method approach, using optical and scanning electron microscopy, X-ray microdiffraction, Raman spectroscopy, and electron probe microanalysis, reveals that particle morphologies trace the flow of opal-forming colloidal suspensions and document syn- and post-depositional deformation. The micromorphology of amorphous silica pseudomorphs suggests that the volume-preserving replacement of non-silicate minerals proceeds via an interface-coupled dissolution precipitation process. We conclude that colloid flow and post-depositional shearing create but also destroy natural photonic crystals. Contrary to previous studies, our results indicate that purely gravitational settling/ordering is the exception rather than the rule during the formation of three-dimensional periodic sphere arrays in the highly dynamic colloidal suspensions of chemically weathered clastic sediments. [ABSTRACT FROM AUTHOR]