This paper summarizes the five-year monitoring works that were conducted for the Nagaragawa Estuary Barrage between 1995 and 1999 from administrative point of view including environmental studies during a pre-construction stage. The monitoring was carried out by the Ministry of Construction (recently reorganized into the Ministry of Land, Infrastructure and Transport, or MLIT) and Water Resources Development Public Corporation under real operational stage. The post-construction stage monitoring was conducted under the guidance of the Nagaragawa Estuary Barrage Monitoring Committee, and the monitored results were made public annually by reports. Monitoring covers important items for fauna and flora of brakish water zone, for instance, dissolved oxygen, biological oxygen demand, salinity, water temperature, chrolophyll A, bottom sediment, fishes and anodromous fishes, shell fishes, reed beds, and so on. This paper describes how the system of monitoring was developed and the monitoring proceeded with several changes of target species and monitoring locations. Monitored results are reflected in the management of the lower reach of the Nagara River. In the fiscal year of 2000, the MOC (now MLIT) and Water Resources Development Public Corporation took over the monitoring. A new series of monitoring in a follow-up stage is undertaken under the guidance of the Chubu Region Dam and Estuary Barrage Management Follow-up Committee (Dam Subcommittee).