Geologically, Darwin Island derives from the remains of an extinct volcano, which is believed to have last erupted approximately 400,000 years ago.  There are currently two theories revolving around the formation of the lineament, in which both Darwin and Wolf are situated.  The first theory states that the magma rising from the mantle plume that forms the main Galapagos Islands has been channelled towards the Galapagos Spreading Centre.  The second theory claims that there has been a separate rise in magma, resultant from stress in the ocean lithosphere by a transform fault.  Darwin's lava flows are homogenous, due to its relatively young age, with a similar chemical composition to those of the Galapagos Spreading Centre.

Historically, it is believed that Darwin has experienced at least two eruptive periods of two tuff layers, separated by plagioclase ultraphyric basalt.  Evidence also suggests that Darwin was much a substantially larger edifice - although over the years, significant erosion has inevitably occurred.

Probably one of Darwin's most symbolic features is that of the natural rock arch, a landmark which lies less than a kilometre off the main island. This arch at one stage would have been part of a larger structure.

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