In 2013 Shelter Inlet had the coldest bottom waters in all of Clayoquot Sound by half a degree celsius. Its temperatures tend to be close to that of Herbert and Sydney, which boarder it. The water column showed even stratification except at the mouth where some warmer ocean water came in the inlet on its surface.

Shelter inlet had solid 31.5 PSU salinity from 30 m down to the bottom. This shows significantly less stratification than nearby Herbert Inlet, which showed more layers and only reached a max of 31 PSU. The only stratification in Shelter appears on the surface water. From the head of the inlet where fresh water comes in from rivers the lowest readings are found at 28.5 PSU.

Density mirrors temperature with its neat layers of stratification. Its highest density appear at 78 m down and its lowest at the surface near the head where fresh water flows into the inlet. This is very similar to findings in nearby inlets.

Dissolved oxygen has less even layers of stratification, but generally has the lowest levels at the bottom where production is low, and higher levels at the surface where production is higher.

Fluorescence represents productivity, which indicates phytoplankton. Fluorescence only occurred in the surface water just passed 20 m. The layer gets as thin as less than 10m deep, but runs the length of the inlet.

Transmissivity represents solid particles suspended in the water, but not the identity of the matter. The largest quantities can be found flowing in from the mouth of the inlet and in its bottom waters. The particles at the surface correspond with the location of fluorescence, so those are most likely phytoplankton and the rest decaying matter.