The Water Framework Directive (WFD) requires the improvement of water quality in the EU and the assessment of the transitional waters ecological status considering the fish component of the ecosystem. In the WFD, the dissolved oxygen (DO) is considered as one of the physico-chemical quality elements that support the biology and have to be monitored. Estuaries are particularly essential to fish as refuge area, habitats for reproduction, nursery grounds and migration routes but they are impacted by multiple anthropogenic disturbances. Hypoxic threshold is largely characterized by a DO content of 2 mg L-1 whereas the median lethal concentration is about 2.45 mg L-1 for aquatic organisms. Since 2005, this parameter is monitored in the Gironde Estuary thanks to the continuous monitoring MAGEST network that has recorded several summer borderline hypoxic situations (DO close to 2 mg L-1) and a 7 days-long hypoxic event (DO < 2.45 mg L-1) in July 2006 with a minimum measured value of 1.22 mg L-1. Biological responses to hypoxia depend on the period, intensity and extent of these events. Shads, Alosa fallax and Alosa alosa, and some shrimp developmental stages, are among the most sensitive species to hypoxia in the Gironde Estuary. A behavioral study was performed on shad juvenile and allowed to establish the DO threshold that could impact their downstream migration occurring from July to early October. Water temperatures in summer 2006 are the highest recorded in the period 2005-2012 with values higher than 28°C. Almost 43% of conditions (DO thresholds at 20°C and 25°C) are critical to shad juveniles during their migration period in 2006. More than 940 hours reached critical values including 460 hours that would result in the death of individuals. Although the fish taxa appear to be more sensitive towards hypoxia, the crustacean taxa show also a strong sensitivity in the early ontogenic stage and on eggs-bearing females. Because shrimp is a major component of the estuarine food web, this taxon appears as a promising indicator of ecosystem dysfunction.