This study aims to determine the condition of water quality based on some physical and chemical factors in the environment to support agro-ecosystem coastal and small island of East Kutai Regency. Collection of field data was conducted on 13 to 16 October 2012 at four districts is Sangkulirang district, Sandaran district, Bengalon district and Teluk Pandan district. Water quality data is measured directly in the field of temperature and salinity, while pH, TSS (Total Suspended Solid) and TDS (Total Dissolve Solid) by analyzing in the laboratory of Water Quality Mulawarnan. The result showed that the temperature ranged from 27.5 to 28.5 oC. The lowest temperature at station MP 15 (Labuan Kelambu) and the highest at Station MP 19 and 20 (Miang Besar Island) Sangkulirang district. Surface temperature conditions are deemed natural conditions. Salinity range from 25 – 35 o/oo. Lowes salinity found in the area around the estuary Pulau Seribu, Sangkulirang district and Bengalon, Bengalon district. Water pH ranged from 7.7 to 8.2. Categorized pH value range is still good for the life of the organism 7 – 8.5. The content of TSS in the coastal waters around Kutim including clear until close category cloudy with TSS values ranging from 9.0 to 67 mg/L. Most locations TSS measurement showed a small (<20 mg/L), which is a clear water conditions. In general, this condition is still good, especialy for mangrove growth in the amount of 79 mg/l and class III water quality standards. The Content of TDS ranges between 25.065 – 43.929 mg/L. Such a condition is that the content is still very narural, so it can be expected around the coastal water of the East Kutai is still very natural, so it can be expected around the coastal waters of the East Kutai is still verry natural.