The monsoon season usually occurs between June and October. The Mekong River is affected by the annual flood pulse, in September and October, when water levels are particularly high. During this period, fish migrate downstream to reproduce and high volumes of water bring nutrient-rich sediments to Tonle Sap Lake and to the floodplains in the Mekong Delta in Vietnam. This annual process is beneficial and necessary to support fisheries and agriculture in the Lower Mekong Basin. Despite the benefits of the flood pulse, it too can be a risk to the community. Annual floods can take lives and destroy agricultural land.

During the dry season between December to May, there is minimal precipitation and any water that flows down the Mekong River comes solely from the Tibetan Plateau. When the water level is low, salt water from the South China Sea will intrude into the Mekong Delta, making it too saline for crop cultivation.

Both floods and droughts are part of the natural process, and they occur in many parts of the world. Bearing this in mind, any strategies to prevent flood- or drought-related losses should take both the human aspect and ecological aspect into consideration.