Planktonic communities from Juan de Nova lagoon were submitted to a single exposure of diuron or naphthalene in triplicate outdoor 40-L mesocosms for 5 days. The study followed the temporal changes of the assemblages by determining abundances and taxonomic level of microbial (heterotrophic prokaryotes, picocyanobacteria, heterotrophic protists and phytoplankton) and metazooplankton communities. Exposure to both contaminants did not result in significant changes in phytoplankton abundances. Microscopic identification demonstrated the dominance of Bacillariophyta (mostly Chaetoceros tenuissimus) accounting for more than 95% of the microalgae detected in all mesocosms. Using 18S rRNA metabarcoding, temporal changes in the proportion of eukaryotic operational taxonomic units (OTUs) were highlighted for most taxonomic groups. Diuron had no significant effect on the abundance of eukaryotic picoheterotrophs, ciliates, whereas naphthalene had a significant positive effect on heterotrophic prokaryotes. Metazooplankton was not significantly modified under contaminant exposure, except for copepods nauplii in presence of diuron. Multivariate analysis indicated significant responses of communities linked to the experimental time and conditions. The analysis also revealed a modification of the trophic relationships among communities over time, from a dominant multivorous food web after 48 h towards a reduced microbial loop after 120 h of experiment time.