This study was conducted to investigate the nutrient distribution and controlling factors in small stream estuaries. The seasonal variations of nutrient concentration (nitrate, ammonium and phosphate) were observed from 2010 to 2012 in the three streams located in Dang-hang (closed estuary: Go-seong, open estuary: Gu-man and Ma-am). The nutrient concentrations in Go-seong were significantly higher than other estuaries, because Go-seong is relatively large and has large nutrient load from the watershed. The dyke located at the estuary, also, caused the high nutrient concentration by reducing the dilution and increasing residence time. In all three streams, nitrate concentration was high at upstream and decreased toward the downstream, because high load of nutrient input were located at upstream. Dilution and biogeochemical removal toward the downstream also caused the trends. Especially, denitrification, a typical nitrogen removing process showed clear tendency of gradual decreasing from upstream to downstream. However, Ammonium and phosphate concentrations were high at upstream and decreased toward the downstream only when the nutrient loads from the rivers were high. Nutrient concentrations were low in summer and high in winter. Freshwater discharge in summer caused a decrease of the residence time and increase of the transport of nutrients to downstream and reduced the nutrient concentrations in the estuary. Nutrient removal by the biological production during high temperature periods also affected the low nutrient concentrations. Small stream estuaries showed distinct nutrient dynamics. It is necessary to understand these characteristics in order to properly manage the small stream estuary.