The climate of Jaffna peninsula is considered to be tropical monsoonal with a seasonal rhythm of rainfall. The temperature ranges from 26 C to 33 C. Annual precipitation ranges from 696 mm to 1125 mm. The north east monsoon rain (October to January) accounts for more than 90 % of the annual rainfall.

The city is surrounded by Jaffna Lagoon to its west and south, Kokkuvil and Thirunelveli to the north, and Nallur to the east. Jaffna peninsula is made of limestone as it was submerged under sea during the Miocene period. The limestone is grey, yellow and white porous type. The entire land mass is flat and lies at sea level. Within one mile of the city center is the island of Mandativu which is connected by a causway. Palmyrah groves can be seen where land has not been used for construction. Other notable vegetation is a leafless shrub called talai (alae africana) and koddanai (oleander)

Jaffna features a tropical rainforest climate with no true dry season month. Jaffna has the highest average temperature in Sri Lanka – 83 °F (28 °C). The temperature is highest in the months of April – May and August – September. The temperature is coolest in December – January. The annual rainfall is brought in by the North East monsoon and it varies from one place to the other and also from year to year. The average rainfall is 50 inches in the western part of Jaffna peninsula.