A grizzled skipper and a spirited missionary take on the Germans in Africa during World War I.

In September 1914 in the German East African village of Kungdu, British Reverend Samuel Sayer and his spinster sister Rose lead prayers at the makeshift First Methodist Church. The natives struggle to follow the English psalm, but race outside when they hear Canadian Charlie Allnut's ancient launch the African Queen chug into the village, laden with mail and goods. Though conscious of his lower social standing, Charlie lunches with the Sayers, who delicately ignore his rumbling stomach. Before leaving, he informs them about the encroaching war in Europe, and although the Sayers are frightened, they refuse to desert the village. Only hours later, however, German troops invade Kungdu, imprison the natives and burn down the huts. By the time the smoke clears, Samuel has begun to lose his mind from shock and grief. He soon collapses, unintentionally wounding Rose by raving that their attraction to missionary work grew out of a lack of more attractive social options. When Charlie returns to the destroyed village the next day, he finds Samuel dead, and helps Rose bury him. She then accepts Charlie's offer to hide from the Germans on his boat. Once they are on the river, Charlie explains that the Germans have positioned a heavily armed steamer, the Louisa , at the mouth of Lake Tanganyika to block British troops. Rose immediately forms a plan to attack the Louisa by crafting torpedoes out of explosives and an oxygen tank, strapping them to the African Queen and ramming into the steamer. Charlie tries desperately to dissuade her, describing the German fort and impassable rapids they will have to face along the way, but Rose's determination eventually shames him into agreeing to the plan. After they set sail, he teaches Rose how to read the river, and they negotiate how to bathe in private. That night, a pouring rain forces Charlie to seek shelter under Rose's tarpaulin, and after at first banishing him, Rose softens and allows him to sleep near her. They reach the first set of rapids the next afternoon, and Charlie's hopes that the death-defying experience will frighten Rose are dashed after she proclaims it the most stimulating physical experience she has ever had. At night, a frustrated Charlie taps into his gin reserves and later rants drunkenly that he will not sail any farther, calling Rose a "skinny old maid." He awakes the next morning to find her pouring each of his gin bottles into the ocean. Hours later, he begs her to speak to him, and she finally reveals that it is his refusal to sail which has infuriated her. Charlie yells but then quickly backs down, agreeing to accompany her while doubting their chances for success. Their first obstacle is the German fort, where the soldiers open fire on the African Queen . The engine is hit, but Charlie repairs it and they sail on. Immediately afterward, they reach another set of rapids. Rose struggles to steer while Charlie races to keep the engine stoked, and although they are badly pummeled, they miraculously reach calm waters. Thrilled, Charlie and Rose fall into an embrace which quickly becomes romantic. Later, as they declare their love, they finally learn each other's first name. They then sail peacefully past exotic flora and fauna until they hit a waterfall, which damages the rudder. Although Charlie despairs, Rose devises a plan to weld a new rudder, and days later, the boat is fixed. Just miles down the river, however, they are attacked by a horde of mosquitoes, which terrifies Rose and forces them to stay in open water. Within days, they become lost in the stagnant shallows. Thick reeds bog down the boat, forcing Charlie to pull it through the water. When he finally boards again, exhausted, he finds leeches covering his body, and even though he is shaking with revulsion, he must return to the water to keep the boat moving. Hours later, they reach land, where Charlie feverishly tells Rose they may not make it but that he loves her. They both collapse into sleep, and during the night, a fresh rain sweeps the launch downstream onto Lake Tanganyika. They awaken to find the Louisa only miles away, and retreat into the reeds to hide. By the next day, they have discerned the ship's sailing pattern and Charlie makes the torpedoes. They set out on their attack that night, but a sudden storm capsizes the launch and Rose and Charlie are separated in the dark. Charlie is imprisoned by the Germans and, not wanting to live without Rose, accepts his sentence of hanging. Just then, however, Rose is brought in, and when she hears that Charlie is to be killed, proudly admits their whole scheme to the soldiers. Before they are hanged, Charlie requests that the captain marry them, and just as the service ends, the African Queen surfaces, hits the Louisa and explodes. Floating together in the water, the newlyweds see the boat's nameplate, realize that their plan has succeeded after all, and happily swim toward the shore.