Etymology
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chowder (n.)

"thick fish soup," 1751, American English, apparently named for the pot it was cooked in: French chaudière "a pot" (12c.), from Late Latin caldaria "cooking pot" (source of Spanish calderon, Italian calderone), from Latin calidarium "hot bath," from calidus "warm, hot" (from PIE root *kele- (1) "warm").

The word and the practice were introduced in Newfoundland by Breton fishermen and spread from there to the Maritimes and New England.

CHOWDER. A favorite dish in New England, made of fish, pork, onions, and biscuit stewed together. Cider and champagne are sometimes added. Pic-nic parties to the sea-shore generally have a dish of chowder, prepared by themselves in some grove near the beach, from fish caught at the same time. [John Russell Bartlett, "Dictionary of Americanisms," 1859]

 The modern form of it usually features clams. In New England, usually made with milk; the Manhattan version is made with tomatoes. The derogatory chowderhead (1819) is a corruption of cholter-head (16c.), from jolt-head, which is of unknown origin.

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*kele- (1)

kelə-, Proto-Indo-European root meaning "warm." It forms all or part of: caldera; calid; Calor; caloric; calorie; calorimeter; cauldron; caudle; chafe; chauffeur; chowder; coddle; lee; lukewarm; nonchalant; scald (v.) "afflict painfully with hot liquid or steam."

It is the hypothetical source of/evidence for its existence is provided by: Sanskrit carad- "harvest," literally "hot time;" Latin calor "heat," calidus "warm," calere "be hot;" Lithuanian šilti "become warm," šilus "August;" Old Norse hlær, Old English hleow "warm."

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bouillabaisse (n.)
type of fish chowder, 1845, from French bouillabaisse (19c.), from Provençal bouiabaisso, boulh-abaisso, a compound of two verbs corresponding to English boil (v.) + abase (in the original sense of "to lower").
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clam (n.)

bivalve mollusk, c. 1500 (in clam-shell), originally Scottish, apparently a particular use of Middle English clam "pincers, vice, clamp" (late 14c.), from Old English clamm "bond, fetter, grip, grasp," from Proto-Germanic *klam- "to press or squeeze together" (source also of Old High German klamma "cramp, fetter, constriction," German Klamm "a constriction"), possibly from a PIE *glem- or *glom- "contain, embrace" (see glebe).

If this is right then the original reference is to the shell. Clam-chowder attested from 1822. To be happy as a clam is from 1833, but the earliest uses do not elaborate on the notion behind it, unless it be self-containment.

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