Climate in the Turtle Islands is typified by warm and humid conditions, with no pronounced wet and dry seasons. Data from the nearby Sandakan, Sabah weather station (1956-1957) indicates a mean minimum temperature range from 22 to 24C and a mean maximum temperature range from 29 to 33C. The hottest months are from March to September and the coldest from October to February. A mean relative humidity of 70% is due to high temperature, high rate of evaporation, and heavy rainfall.

Rainfall is evenly distributed throughout the year at an average of 18.04 mm. Monthly rainfall data collected at the Sandakan station over a period of 52 years (1905-1957) shows total annual rainfall to be 3,138.93 mm while data from the Cagayan de Tawi-Tawi station shows an annual total of 2,286.2 mm.

The climate of the Turtle islands is influenced by the Northeast and Southwest monsoons which prevail from November to March, and June to September, respectively. The North Pacific Trades dominate during the transition between the two monsoons (PAG-ASA, 1987). The prevailing wind is easterly at two knots.

Based on the meteorological data from Cagayan de Tawi-Tawi, the wettest period in the southwestern Sulu Sea is during the transition season (October and November), while data from Sandakan indicates high rainfall during the early part of the Northeast Monsoon (December and January). The meager rainfall data gathered from Baguan shows a similar rainfall pattern with that of Sandakan which has the highest rainfall during the months of December and January.