Estuaries are crucial ecosystems where human activities deeply affect numerous ecological functions. Here we present a survey dataset based on the monitoring of fish nursery grounds of the Seine estuary and eastern bay of Seine collected once a year using a beam trawl during three distinct periods (1995-2002, 2008–2010 and 2017–2019). The surveys happen at the start of autumn in order to maximize the catchability of juvenile fish. The beam trawl mainly targets benthic and demersal species on a study area that extends over 600 square kilometers. The dataset includes abundance and densities of 161 species for 634 hauls performed around 40 stations each year. These data can be used by fishery scientists and ecologists motivated by early life stages of commercial species or by the impact of human disturbances, such as harbor developments, on estuarine communities.