The sustainability of mangrove ecosystems requires a knowledge of their spatiotemporal variability as a function of regional properties. The unique coastal ecosystems of the mangrove belt along the coast of the Guianas in South America are influenced by cycles of a massive accretion of mud supplied by the Amazon River and wave induced erosion. This study characterized, for the first time, how benthic infaunal assemblages, as proxies of mechanisms of mangrove resilience, were structured by the natural growth track of Avicennia germinans dominated mangroves in French Guiana. We sampled 4 mobile mud stations and 27 consolidated mud stations distributed over 9 tidal transects from bare to vegetated mudflats colonized by young mangroves during the dry season. We collected a complete dataset of sediment and vegetation variables together with the benthic meso- (>0.25 mm) and macrofauna (>1 mm). We used a combination of eigenvector based multivariate analyses and variance partitioning on this multiple set of variables to identify which environmental variables likely drive the benthic diversity patterns. Mangrove early development increased the alpha and beta diversities of the infaunal communities for the two size classes. A total of 20–30% and 7–12% of the beta diversity are explained by linear and nonlinear spatial variables, respectively. However, 7% to 9% of the variance partioning could be determined by other biotic/abiotic variables, biological interactions or neutral processes, not described here. This study has highlighted the necessity of taking into account mangrove dynamics at suitable spatial scales for benthic biodiversity evaluation and mangrove management or restoration plans.