Estuary is one of the important ecosystem located on the coast. Where of the decomposition cycle nutrient. The available of nutrients in the waters can be an indicator of water fertility. In this case, the element nutrient which is visible content of organic matter in sediment Wiso Estuary, Jepara. The nutrients are crucial to the survival of organism. The reseach was conducted on March – April 2016 in order to determine the total bacteria, the amount organic matter and relations between total bacteria and organic matter in the sediment Wiso estuary, Jepara. The method used in this research is descriptive explanation. Sampling was conducted at Wiso estuary at three observation stations. Station I is the upstream of Wiso estuarine stream. Station II is a center part of Wiso estuarine stream. Station III is the final part of Wiso estuarine stream which is directly adjacent to the beach. Total bacteria in bottom sediment Wiso estuarine, Jepara ranged between 3,3 x 105 cfu/ml up to 1,2 x 107 cfu/ml. Content of Organic Matter in bottom sediment Wiso estuarine, Jepara ranged between 7,12 % up to 16,57 %. Organic matter was not correlation with total bacteria (P > 0,05) in bottom sediment Wiso estuarine Jepara.