Nurseries are crucial habitats that play an important role for many marine fish species; which rely on them to complete their life cycle. Juvenile stages of dab (Limanda limanda), plaice (Pleuronectes platessa) and sole (Solea solea) present in the English Channel are common in the Seine estuary nursery grounds. To further explore the estuary's nursery function, we investigated the heterogeneity in spatial distribution patterns of these three flatfish at their juvenile stage, between 1996 and 2019. We used geostatistical indices and multivariate analyses to demonstrate species specific spatiotemporal dynamic. Sole favoured the most upstream part of the nursery, dab was found in the most marine areas, and plaice preferred the southern coast. We then performed clusters analysis based on spatial indices and spatial patterns extracted from a Minimum/Maximum Autocorrelation Factor (MAF). We showed that the average positions of the three flatfish species were stable across time. Each flatfish appeared to have its own spatial preference inside the nursery. No temporal variability in the spatial pattern nor trend was found that would correspond to the major stress imposed on the community by harbour development within the 2000–2005 period. We conclude that segregation of the juveniles of the three species within the nursery may reflect different ecological needs and underlying mechanisms to minimise interspecific competition.