Dumaguete has a land area of 34.26 km², situated on the plains of the southeastern coast of Negros Oriental near the mouth of the Banica River. Of the province's 20 municipalities and 5 cities, Dumaguete is the smallest in terms of land area. It is bounded on the north by the municipality of Sibulan; on the south by the municipality of Bacong; and on the west by the municipality of Valencia. As a coastal city, it is bounded on the east by the Mindanao Sea and the Tañon Strait, serving as a natural border to the neighboring provinces of Cebu and Siquijor.

The city's topography is generally flat from two to six kilometers from the shoreline. It slopes gently upwards to the adjoining municipality of Valencia. The highest ground elevation is located at the boundary of the municipality of Valencia, about one hundred meters above mean sea level. About 93% of the land have slopes of less than 3%. The remaining areas have 3% to 5% slope.
Dumaguete is politically subdivided into 30 barangays, all classified as urban. The eight barangays in the city's downtown area are known primarily by number. The smallest barangay is Barangay 4 with an area of only 5.11 hectares, while the biggest barangay is Barangay Banilad with 362.71 hectares.

Dumaguete has two seasons, namely; the dry and the wet seasons. The wet season covers the period from June to November, and the dry season starts from December to May, the hottest being April and May. The average maximum temperature is 34.3 °C and the average minimum temperature is 22.9 °C for the past years. The relative humidity of the locality for the past years was 78¾% with the month of December registering the highest.

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