Estuarine environments fulfill the ecological function of nurseries for the juveniles of many fish species. Shallow areas, warm, productive, and offering shelter from predators are particularly suitable as a kindergarten. In tidal systems, the most productive areas lie in the intertidal zone and the spatial distribution of nurseries changes hourly with the rising or receding water level. To access them, fish juveniles thus have to effectuate daily migrations between low-tide resting habitats and high-tide feeding habitats. The functional connectivity between these habitats, crucial for the juvenile survival and growth, is influenced by the landscape resistance to movement. The latter integrates a row of both dynamic and structural factors such as the intensity and directionality of flow or the presence of natural and anthropogenic barriers. Altogether a particularly high spatial and temporal variability in functional connectivity is characteristic of estuarine landscapes exposed to tides. We analyze the nursery habitat accessibility for the juveniles of the European seabass (Dicentrarchus labrax), a marine species which effectuates migrations to coastal and estuarine nurseries during its first 3-4 summers. Our study system is the macrotidal Seine estuary at the French Atlantic coast which remains an important nursery area for the study species in spite of heavy modification through diking and artificial channel deepening for navigation. Submersible dikes play a particularly important role for the temporal variability in functional connectivity of the Seine estuary: they act as a barrier for a part of the tidal cycle duration and, at a certain water level, once submerged, can be crossed by the fish during the rest of the tidal cycle. Specific goals of our work were to: 1) evaluate the spatio-temporal distribution of seabass nursery patches and quantify the probability of their access by juveniles during tidal cycles; 2) identify key factors structuring the patterns of functional connectivity in the Seine estuary. We chose to address these goals using GIS-based spatial analysis and a chronological modelling approach, allowing us to capture the temporal changes in both habitat patch distribution and estuarine landscape resistance to movement during the tidal cycle. Several scenarios were tested to compare the effects of different tidal coefficients and juvenile dispersal strategies (passive transport, selective tidal transport, active swimming) on our estimates of functional distances between habitat patches and their accessibility throughout the tidal cycle. Our findings (i) point towards a disruption of connectivity between the north and the south areas of the estuary due to the presence of the submersible dikes and (ii) allow an estimation of the time necessary for the colonization of the estuary by juvenile seabass. We dedicate a special attention to the accessibility of tidal creeks, a habitat particularly valuable for young fish juveniles and due to human activities increasingly disconnected from the main channel of the Seine. We finally discuss the multitude of applications of our approach for both identifying and quantifying accessible functional habitats of interest, testing alternative management scenarios and prioritizing conservation and restoration areas.