Thanupp follows the story of Pratheesh and Treesa, a young couple who settle in a scenic village surrounded by hills and rivers. With the help of Prakasan, Pratheesh finds work as a painter in his company. While the villagers grow fond of the couple, they sense something mysterious about them, especially as they frequently inquire about the location of the village river. The film unravels the deeper story behind their intentions, exploring themes of unwavering social commitment and hidden truths.