We analysed the temporal variability of meiobenthic (meiofauna and protists) abundance and community structure in the sediments of two shrimp farms located in New Caledonia. In each farm, sediment samples were collected weekly from February to June 2006 at two ponds, and analysed for quantity and composition of sedimentary organic matter, meiofaunal abundance, taxa richness and community composition. Independently of the initial conditions, sedimentary contents of biopolymeric C and total phytopigment varied significantly during shrimp rearing, although not consistently in the two ponds. Changes in the quantity and biochemical composition of sedimentary organic matter were associated with changes in total meiofaunal abundance and taxa richness, as well as in total and rare (< 1% of total abundance) meiobenthic community composition. We show that the slight eutrophication of the sediment during the shrimp rearing cycle determined significant effects on the meiofaunal community composition as well as on the relative importance of metazoan vs. protists abundance. The results of this study suggest that the study of meiobenthic communities represents a reliable descriptor of the environmental quality of shrimp farming ponds.