"The Narrow Land", a novelette by Jack Vance, first published in Fantastic, July 1967, available at the Internet Archive. You may have read it in his collection Green Magic, or in The Narrow Land, a Vance collection named after that story.
It starts out describing the life of the main character as a fish who hides from the lake monster,
Most dreadful of all was the ogre who lived in one of the sea-sloughs: a brutish creature with long arms, a flat face and four bony ridges over the top of its skull. On one occasion Ern almost became its victim. Skulking under the roots of the swamp-reeds, the ogre lunged forth; Ern felt the swirl of water and darted away, the ogre's grasp so near that the claws scraped his leg. The ogre pursued, making idiotic sounds, then jerking aside seized one of Ern's playfellows, and settled to the bottom to munch upon its captive.
as he matures he is captured by relatives. There are males, females, and neuters. As they can't quite figure out what he is he is placed with the neuters, but he's more intelligent, driven, and barely fits in.
Changes were taking place; they could not be ignored. The whole of Ern's class lived at the surface, breathing air. Infected by some pale dilution of Ern's curiosity, they stared uneasily landward. Sexual differentiation was evident; there were tendencies toward sexual play, from which the double-crested children, with undeveloped organs, stood contemptuously aloof.
Above Ern's head sounded the mindless howl of a tinkle-bird. Ern darted back into the brush. The bird drifted overhead on clashing scales. Men ran to either side, chased Ern back and forth, and finally captured him. He was dragged to the village, thrust triumphantly up on the platform, among calls of surprise and excitement. The four priests, or whatever their function, surrounded Ern to make their examination. There was a new set of startled outcries. The priests stood back in perplexity, then after a mumble of discussion signaled to the priest-women.
When he reaches puberty and makes sexual advances towards a female
Thoughtfully Ern returned to his cubicle. In due course a One-girl came past. Ern summoned her into the cubicle and made his wishes known. She showed surprise and uneasiness, though no great disinclination. "You are supposed to be neutral; what will everyone think?"
he is cast out.
A monitor looked into the cubicle, to stare dumbfounded. "What goes on here?" He looked more closely, then tumbled backward into the compound to shout: "A Freak, a Freak! Here among us, a Freak! To arms, kill the Freak!"
Ern thrust the girl outside. "Mingle with the others, deny everything. I now feel that I must leave."
In exile he finds another person like himself, and he discovers that a male and female egg can merge (chimerism) to create a neuter, with himself being the merge of two male and one female egg.
"You are obviously a 'Three'," said his host. Unlike the neuter Twos, Threes are notably masculine, which explains your inclinations for the One-woman. Unluckily there are no Three females." He looked at Ern. "They did not tell you how you were born?"
"I am a fusion of One-eggs."
"True. The One-woman lays eggs of alternate sex, in clutches of three. The pattern is male-female-male; such is the nature of her organism. A sheath forms on the interior of her ovipositor; as the eggs emerge, a sphincter closes, to encapsulate the eggs. If she is careless, she will fail to separate the eggs and will put down a clutch with two eggs in contact. The male breaks into the female shell; there is fusion; a Two is hatched. At the rarest of intervals three eggs are so joined. One male fuses with the female, then, so augmented, he breaks into the final egg and annihilates the other male. The result is a male Three.
He contemplates what the merger of four eggs would be like, but realizes such a merge created the lake monster. Towards the end of the story he sets out to place two female and one male egg together to create himself a partner.
Once more in the hall Mazar arranged the eggs on a stone settle. He made a sound of satisfaction. "In each clutch are two round eggs and one oval: male and female; and we need not guess at the combinations." He reflected a moment. "Two males and a female produce the masculine Three; two females and a male should exert an equal influence in the opposite direction . . . There will necessarily be an excess of male eggs. These will yield two masculine Threes; possibly more, if three male eggs are able to fuse." He made a thoughtful sound. "It is a temptation to attempt the fusion of four eggs."
"In this case I would urge caution," suggested Ern.
Mazar drew back in surprise and displeasure. "Is your wisdom so much more profound than mine?"
Ern made a polite gesture of self-effacement, one of the graces learned at the Two school. "I was born in the shallows, among the water-babies. Our great enemy was the ogre who lived in a slough. While I searched for eggs, I saw him again. He is larger than you and I together; his limbs are gross; his head is malformed and hung over with red wattles. Upon his head stand four crests."
Mazar was silent. He said at last: "We are Threes. Best that we produce other Threes. Well then, to work."