A grain size analysis (including the carbonate fraction) was performed on sediment samples from each of the following environments of Bahia la Choya: tidal flat, spit, beach, and estero. The sediments of the tidal flat have an average grain size of 2.88 phi, range from very well sorted to moderately well sorted, and have a carbonate shell fraction ranging from 1 to 30%. The spit sediments have an average grain size of 0.96 phi, are moderately to poorly sorted, and have a carbonate shell fraction of approximately 50%. The beach sediments have an average grain size of 1.22 phi, range from poorly sorted to moderately well sorted, and have a carbonate shell fraction of approximately 48%. The sediments of the estero average 39% sand, 40% silt, and 20% clay. The carbonate fraction in the estero is approximately 25%. The noncarbonate fraction in all the environments is made up of feldspar, quartz, biotite, heavy minerals, and igneous rock fragments.

The major source for the sediment is the Pelican Point granite on the south side of the bay. Pleistocene rock in and around the bay provides a second source of sediment and volcanic rocks to the north may also contribute to the sediment.