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The Rattaphum Catchment comprises four major hydrogeomorphic units: mountains, footslopes, plains and inland swamps around a lake system. The area accommodates three main agro-ecosystems: vegetable, rubber and fruits. During the high-rainfall period, groundwater levels rise near to the soil surface in all agro-ecosystems. The high water levels remain for 3–4 months in the coastal plain, while in other areas the groundwater level fluctuates according to the intensity of rainfall events during the 2–3 months of the rainy season.Groundwater salinity is higher near Songkhla Lake and decreases rapidly inland. It is generally lower near streams. Salinity is also lower during periods of higher recharge, increasing slightly during the dry season due to leaching of chemicals from the agricultural areas. In the saturated sandy soils with high hydraulic conductivity and in the vegetable agro-ecosystem areas with high water levels, the NO3 level in groundwater always exceeds the WHO standard. Variations in NO3 levels are closely related to patterns of landuse, with higher nitrate levels commonly found in vegetable areas and lower levels associated with fruit and rubber tree plantations. Nearly all groundwater and surface water is contaminated by coliform bacteria, with the level of contamination controlled by groundwater levels, the amount of rainfall and farm activities. Vegetable agro-ecosystems, which have the most intensive cropping system, were found to be the most polluted. In all of the agro-ecosystems, the most polluted period coincided with the first series of rainfall events.