South Nunukan District has a complex ecosystem which has the river, terrestrial, coastal and oceanic ecosystems, and has been demarcated by the Government of The Nunukan Regency for agricultural purposes. This research was conducted to determine the preliminary environmental baseline of agricultural activities that have been and will take place in this region. Methods of measuring environmental quality were carried out by (1) measuring water quality by taking water samples at four locations and tested in a laboratory; and also measuring aquatic biota by taking samples in rivers and testing at a laboratory, (2) measuring air quality at three sample locations using an air quality meter, and noise using a sound level meter, (3) measuring soil quality by taking five samples at the study site and conducting soil quality testing in the laboratory. The result of this study concluded that this area is suitable to be used as an agriculture and plantation area by adding various engineering technologies and fertilizing. This is supported by the results of water, air, noise and soil quality tests from several samples showing the average within and bellow the permissible limit (WPL and BPL). For a small number of parameters that do not meet quality standards (APL), environmental engineering efforts need to be done.