Productive and ecologically highly valuable ecosystems, macrotidal estuaries are also characterised by complex habitat and connectivity dynamics driven by tidal and freshwater influence. Organisms living in these constantly changing systems have to match their movement patterns to the shifting habitat mosaic using available windows of connectivity to access habitat patches of interest. This appears particularly important for the juvenile stages of many fish species colonising shallow and intertidal areas of the estuaries as summer nurseries. We apply tools from landscape ecology to investigate the estuarine habitat and connectivity dynamics on the example of juvenile seabass (Dicentrarchus labrax). We test under which conditions spatio-temporal bottlenecks to estuarine nursery colonisation may emerge for this species in a human-modified estuary. Combining a hydrodynamic model of the Seine estuary with remote sensing data allows us to capture structural changes in habitat availability and connectivity at the estuarine scale and at a fine spatio-temporal resolution. With chronological least-cost modelling of successive tidal steps, we assess patterns of nursery accessibility and estimate tidal colonisation fronts for different mobility scenarios. We show that, at certain hydrological conditions, tidal water level variation causes local disruptions of habitat availability and connectivity, creating temporary bottlenecks for seabass juveniles’ movement. Fish mobility appears determinant for their vulnerability to these connectivity disruptions. Our approach allows for quantitative assessment and visualisation of riverscape complexity related to tidal dynamics. It is applicable to other highly dynamic ecosystems, where the mobile nature of connectivity and habitats needs to be integrated into conservation and management planning.