Younger Lagoon Reserve sits on the first of a series of marine terraces that are visible from UCSC's Coastal Science Campus.  The first marine terrace was formed approximately 100,000 years ago as a result of the uplifting of land caused by plate tectonics, as well as climatic changes facilitating a lowering of sea level.  These marine terraces form a step-like series of flatlands or benches that ascends the seaward slope of Ben Lomand mountain like a gigantic staircase.

The bedrock underlying the reserve is Santa Margarita Sandstone and Santa Cruz Mudstone.  

Mapped soil types on the reserve include: Elkhorn Sandy Loam (0-2% slope, hydric soil), Elkhorn Sandy Loam (2-9% slope), and Watsonville Loam (0-2% slope, hydric soil)