Water temperature is an important determinant of the growth and development of malaria mosquito immatures. To gain a better understanding of the daily temperature dynamics of malaria mosquito breeding sites and of the relationships between meteorological variables and water temperature, three clear water pools (diameter × depth: 0·16 × 0·04, 0·32 × 0·16 and 0·96 × 0·32 m) were created in Kenya. Continuous water temperature measurements at various depths were combined with weather data collections from a meteorological station. The water pools were homothermic, but the top water layer differed by up to about 2 °C in temperature, depending on weather conditions. Although the daily mean temperature of all water pools was similar (27·4–28·1 °C), the average recorded difference between the daily minimum and maximum temperature was 14·4 °C in the smallest versus 7·1 °C in the largest water pool. Average water temperature corresponded well with various meteorological variables. The temperature of each water pool was continuously higher than the air temperature. A model was developed that predicts the diurnal water temperature dynamics accurately, based on the estimated energy budget components of these water pools. The air–water interface appeared the most important boundary for energy exchange processes and on average 82–89% of the total energy was gained and lost at this boundary. Besides energy loss to longwave radiation, loss due to evaporation was high; the average estimated daily evaporation ranged from 4·2 mm in the smallest to 3·7 mm in the largest water pool. Copyright © 2008 John Wiley & Sons, Ltd.