Connectivity in aquatic systems is often related to abundance and permeability of physical barriers, such as dams, which delay or impede movements of biota with important consequences for aquatic biodiversity. Water quality may, however, also control connectivity between essential habitats. In macrotidal estuaries, Estuarine Turbidity Maxima (ETM) have a strong impact on water quality because of the low oxygen concentration occurring as a response to the related high bacterial and low photosynthetic activities. In this study, we assess Allis shad estuarine spawning migration in 2011 and 2012 in the Loire River (France) where the ETM occurs at spring and summer. Using an acoustic telemetry array, we show that trans-estuarine migration is inhibited during hypoxic episodes in the middle part of the estuary. Shad tends to stay in downstream areas, and even at sea, where oxygen conditions are more suitable. Trans-estuarine migration occurs hastily during neap tide when the ETM decreases, both in terms of spatial extent and intensity, inducing a shift in a set of covariates including dissolved oxygen, which increases, and suspended matter, which decreases. In the context of climate warming, ETM are expected to increase with probable adverse implications for shad migration success and doubtless other diadromous populations.