The present study investigated the horizontal and vertical distribution of meiofauna community and Nematoda assemblages on two sandy beaches and two muddy tidal flats in a freshwater Amazon estuary governed by mesotides. Meiofauna density was significantly higher in muddy environments, explained by the higher food availability. On the one hand, there was no difference between sediment layers in both sandy environments, which suggests that individuals must have migrated to layers deeper than 10 cm. On the other, the highest densities and richness in muddy environments occurred in the upper layer due to higher food and oxygen availability in the surface sediment layer, which decreases with depth. Muddy environments differed on both beaches; they had the highest nematode genera densities and richness. This might be explained by the high nutrient enrichment in these environments. There was no significant difference in Nematoda density and richness between zones in any environment, likely due to the small mid-littoral extension (<40 m), which did not favour the high spatial variability of genera. Nematoda density was higher at a depth of 0–2 cm in both muddy environments, explained by the availability of oxygen and food. The high abundance of deposit-feeder genera in muddy environments indicates high organic enrichment, whereas the distribution of trophic types was more homogeneous on the beaches where abiotic factors tended to be more structuring than food availability.