Soil temperature plays very important role in bio chemical processes, root water uptake and also evapotranspiration. This parameter is influenced by environmental factors such as soil moisture content. Recently water shortage has led to adopt intermittent irrigation in Sepidroud Irrigation network in Gilan province, north of Iran. In this method, different submergence depth is applied, which change the root zone (soil and water) temperature. The aim of this study was to investigate the effects of water depth on soil and water temperature in a paddy field. Paddy minis lysimeters, based on completely randomized block design with 5 treatments of constant level of water in the field, (5, 2.5, 0, -5 and -10 cm of the soil surface) in three repetitions. Measurements were including soil temperature at the depths of 5 and 10 cm from soil surface (T5 and T10) and water temperature in the morning and evening. The results showed that T5 was significantly more that T10 .In the morning, water temperature, at and below surface (non-submerged treatments) was lower than soil temperature at the same depth, while in the evening, water temperature was more than soil temperature at the same depth. In daily scale, the water temperature was more than soil temperature at the same depth. Soil temperature was decreased by reduction of soil water depth. In general, the presence of a thin layer of the water on soil surface had a cooling effect on soil but as the water reaches the soil surface, the soil environment becomes much warmer. The reduction of the submergence depth 10 cm below the surface significantly affected the made microclimate of the soil colder, by 1.5◦ Celsius in average.