I'd go with Swim checks and Survival checks, and grant synergy from K/nature.
I'd ignore the Track feat and similar-named class ability; oyster-bearing molluscs aren't noted for their high speeds, and water currents would remove any possible trail long before they had moved more than a few feet.
I'd also ignore the Search skill; Survival makes more sense in terms of identifying the physical characteristics of an individual oyster that is likely to contain a pearl, and once you open a mollusc, the pearl, if present, is very obvious.
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