Earlier it was noted that there was variability in obsidian knapping quality both in original geological exposures and in artifact materials. Obsidian containing heterogeneities such as air bubbles, ash particles, fractures, and occasionally inclusions, were observed in different areas of the Chivay source. While the majority of tools were produced on homogeneous glass (referred to here as "Ob1"), a substantial fraction of flakes and cores, and some tools, were observed in the "Ob2" material containing heterogeneities. When the Ob2 heterogeneities are very small, the knapping quality of the material appears to have not been compromised albeit the material is visibly less pure. A large percentage of the flakes in Block 3 were Ob2 obsidian, while all of the projectile points made from Ob2 obsidian were found in Block 2 in the high puna.

Visual characteristics of Chivay obsidian vary across the source area as well. Colors recorded for artifacts during the phase II lithics analysis included black, grey, transparent (clear), and dark banding was visible in grey and transparent obsidian. Banding resulting from concentrations of tiny magnetite crystals is common in light grey and transparent material. High numbers of transparent flakes were encountered in Block 1 and Block 2, which is along the direct route from the Chivay source to the Lake Titicaca Basin where obsidian from the Colca is known as the "transparent type" (Giesso 2003). Obsidian color and translucence was difficult to quantify during lab analysis, and it is possible that the distinction between grey and clear obsidian may be connected to flake thickness where thinner flakes appear to be less grey due to greater quantity of light passing through.