Kalpeni experiences a tropical monsoon climate (Köppen climate classification *Am*). The weather is generally warm and humid year-round, with temperatures consistently ranging between 25°C and 35°C (77°F to 95°F).
The island receives the bulk of its rainfall during the Southwest Monsoon, which typically lasts from late May to September. During this period, the seas become rough, and boat travel can be heavily restricted. Humidity is high, often hovering around 70-80%. The best time to visit Kalpeni is between October and March, when the skies are clear, the sea is calm, and the weather is pleasantly balmy. As a low-lying atoll, Kalpeni is occasionally vulnerable to tropical cyclones and storm surges.