The north Atlantic coast of South America is influenced by the Amazon River. This coast is considered the muddiest in the world due to the enormous suspended sediment input from the Amazon River. The mobility of the sediment imposes a geomorphological dynamic with a rapid change of shoreline and fast alternation of facies types of the sediment. This study first describes the spatial and functional structure of meiofauna communities of highly unstable intertidal flats along coasts of French Guiana and Suriname in relation to environmental variables. Six sampling sites, composed mainly of muddy sediment, were located 700 km (Kourou) to 1200 km (Nickerie) from the mouth of the Amazon River. The granulometry, chlorophyll a biomass, prokaryote abundance, percentage of organic matter, meiofauna abundance and feeding guilds of nematodes in sediment stations were independent of the distance of the Amazon River mouth and likely were more influenced by the local dynamism of migration of mudbanks. Meiofauna was not more abundant when the sediment was dominated by the finest sediment particles and also when chlorophyll a and prokaryotes, potential prey of meiofauna, were greater. However, as a percentage, small nematodes (biomass of 0.07 ± 0.001 µg ind-1), which are mainly epigrowth-feeders, were more abundant in very fluid mud. Local granulometry and organic matter content appeared to be driving factors of the size structure and functional characteristics of nematodes. Despite the high instability of mudflats, chlorophyll a biomass and meiofauna abundance always tended to be higher toward other world areas. No foraminifera among the six stations of the study were found. Very fluid mud with physical instability of sediment caused a large perturbation to the settlement of meiofauna; the least amounts of chlorophyll a biomass and prokaryotic and meiofauna abundances were found there. Thus, the probable mobility of sediment may select for smaller meiobenthic organisms, mainly epigrowth-feeders nematodes, and disturb the larger organisms in the sediment, and, therefore, they would not permit the settlement of the foraminifera. In addition, no non-permanent meiofauna largely was found in the sediment.