The story commences with the introduction of a young Mexican-Indian pearl diver who is also the protagonist of novella named Kino. Kino is married to Juana, the couple having a baby by the name of Coyotito. They seem to be a peaceful family, having a happy and easy-going livelihood, but all of it changes as Coyotito is bitten by a venomous scorpion. Kino is asked by Juana to get the doctor going to the town, but Kino along with others remind her that they would never be able to bring the doctor to where they lived. Understanding the situation and taking matters into her own hands, Juana decides to carry Coyotito and set off to the doctor on foot. On reaching the doctor’s house, when Juana accompanied by Kino asks for the doctor, his servant tells her and the rest who travelled alongside the family to see what happens, that the doctor is not home. But actually, the doctor is in his home all along but did not want to see Juana’s child because firstly, he was against the race that Kino was from and secondly, Kino could not afford to pay the doctor the amount that the doctor wanted him to.
As Juana takes care of Coyotito to try to heal the swelling that happened due to the bite of the scorpion, Kino goes off to dive into the Gulf in search of oysters with the help of his canoe, while Juana provides brown seaweed to Coyotito’s shoulder. As Kino collects the oysters, he finds an oyster which is oddly much larger than the usual oysters that he generally finds. On opening it, Kino finds a pearl which is about the size of a seagull’s egg. As both Kino and Juana gasp at the pearl, Juana remembers her son and goes to him to have a look when she notices that Coyotito’s shoulder is not swollen anymore. Kino lets out a yell of joy because of the pearl and his son which is heard by other oyster divers as they come to Kino’s canoe quickly.
As the couple return back to their house, stories about them finding the pearl have already spread through the village and town like wildfire. Everyone including the priest and the doctor comes over to visit Kino and Juana, and the priest tells them to thank their lucky stars for finding the pearl. On the other hand, people have already started to think what they would do if they could get their hands on the pearl, including the doctor.
The same doctor who previously refused Kino’s son treatment. The doctor makes a plan to get Coyotito sick again just to gather further profit and get paid more and he succeeds. As the couple seeks help from the doctor again, the doctor provides a special medicine which is supposed to ‘cure’ Coyotito. When it comes to payment, Kino informed the doctor that he would sell the pearl the next day, to which the doctor says that he would like to keep the pearl. Kino refuses this offer from the doctor but his mistake is telling the doctor where he had kept it. Later that night, Kino could hear someone’s presence in the house and is hit in the head. Juana told her husband that maybe the pearl brought bad luck, but Kino disagreed.
The day that Kino decides to sell the pearl, none of the pearl divers in the village goes on their daily routine of work that day. Kino is approached by the first buyer who tells Kino that Kino’s pearl was way to big, for which he would give Kino a small amount of money. To this, Kino rejected the offer, but the first buyer has already informed the other buyers to work together and fix a minimum price. As the three buyers approach the pearl, Kino understands what is actually going on in the current situation. Kino realizes that the three buyers are working together to fool Kino and get the pearl at the lowest price possible. Kino thus decides to go to the city and sell the pearl to other buyers who would pay him more. At this point the third buyer raises his price of buying but is still rejected by Kino. On the other hand, back in the village the relatives of the father of Coyotito discuss if the decision made by Kino was the right one or if he sould have considered the last offer by the final buyer.
That very night Kino is assaulted again by a group of attackers whom Kino does not know. As Juana heard noises inside the house, she went and saw Kino beaten up and bloodied. To this, Juana again urged Kino to get rid of the pearl, throwing it in the ocean and relieving them of the problem once and for all. But Kino still stands by his decision of keeping the pearl and selling it in the capital which would help him manage enough money for Coyotito’s education.
On one of the days following the fateful incident, Juana wakes up early in the morning, when it is still dark and decides to go to the beach with the pearl. Kino seemed to be ready for this as he followed his wife to the beach, and as Juana is ready to throw away the pearl in the ocean, Kino hits Juana in the head which makes Juana unconscious, and just then Kino was once again attacked by some unknown figures which knocks the precious pearl out of his hands. During the situation, Kino manages to stab one of his assaulters but is knocked unconscious.
As Juana wakes up, she finds her husband lying on the beach, with his eyes closed, which a dead body next to Kino. Perplexed in the present situation, Juana finds the pearl which was lying under a rock and hands it to Kino. She also tells him that it is high time that they leave the village because almost everyone would eventually know that Kino killed a man. Following that Juana goes back to get their belongings, and Kino decides to check the canoe. While Kino finds out that there is a huge hole in the canoe, Juana finds that their house had been burnt to a crisp. Juana takes Coyotito and decides to take shelter in the house of Juan Tomas, Kino’s brother, who helps them by making everyone in the village think that Kino and Juana have fled already while they are figuring out how they would actually flee the place. As Juana is not in favor of keeping the pearl at all, Kino desperately believes that the pearl will change their lives for the better.
As the family flee the village, Kino keeps in mind that they are bound to have followers due to the value which the pearl possesses. Since Kino, Juana and their son Coyotito were travelling at night time, they made sure to camouflage themselves and take rest for the day at a certain point, halting. Juana and her son falls asleep and is followed by Kino as well. Kino wakes up with muffled sounds of footsteps, and as he steps out of their hiding spot, he senses that they were being traced by trackers who had been following them.
As they are merely saved from the passing trackers, he sends them up the hill and asks Juana to hide for a moment as Kino distracts the trackers to keep them safe. As Juana refuses to hide, they go up even more through the mountain until Kino along with his family stumbles across a stream, and a cave adjacent to it. He asks his family to take shelter as he proceeds to make false tracks of their marks to distract the trackers. He then goes back to his family to hide along with them.
Failing to find the pearl that day, the trackers decide to spend the night by the spring with a campfire which was very close to the hiding spot of the family. Fearing that they would get caught in the morning, Kino decided to attack the trackers before they could even realize what had happened. As Kino approached and killed all three trackers, he finds out his son was killed from the bullets of one of the trackers.
As the story progresses near a conclusion, the couple walk beside each other carrying a bundle which consisted of their dead son, as people watch them walk as if they were hypnotized in a world of horror, being silent. Juana and Kino walk up to the beach where Kino finally decides to throw the pearl out into the sea and asks Juana to do the honors but Juana insisted that Kino should be the one doing it. Kino finally throws the pearl as far as he could, watching as the pearl descends deep into the ocean for one last time, sinking among the water plants over the sandy bottom.