In this study, we show that the deep‐sea meiofauna community at the Brazilian Equatorial Margin (BEM) is strongly influenced by the Amazon River. Our comparison across four deep ocean basins including Amazon, Pará‐Maranhão, Barreirinhas, and Ceará showed that the former supports a completely distinct meiofaunal community. Meiofaunal richness increased with increasing distance from the Amazon, reflecting changes in sediment proprieties among basins. Total phytopigment content at Amazon sediments was threefold higher than at other basins. The chlorophyll a/Phaeo mean ratio, however, was lower than 1, suggesting a predominant degraded bulk organic matter derived from the Amazon River discharge. Nematode assemblages from Amazon strongly differed from the other basins mostly due to higher genus richness, trophic diversity, and variations in the abundance of Sabatieria, which in turn led into higher dissimilarity values and turnover rate. Furthermore, the bathymetric distribution of nematode assemblages at Amazon and Ceará basins differed significantly among depth zones, especially due to the higher abundance and diversity at Amazon basin. Our findings show that the Amazon River plays a critical role in structuring and shaping the deep‐sea meiofauna and nematode biodiversity at the BEM. Increasing impacts on the Amazon rainforest will certainly affect the amount of freshwater discharge, and the quantity and quality of organic material transported to the Atlantic Ocean, which in turn will have effects on the deep‐sea communities.

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