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In coastal lagoons, many studies indicated that macrozoobenthic assemblages undergo marked temporal fluctuations as related to the strong environmental variability of these systems. However, most of these studies have not assessed the seasonal patterns of these fluctuations and none of them has investigated the consistency of this variation in different areas within the same lagoon system. In this study, we assessed patterns of variation at multiple temporal (date, season and year) scales in two different areas in the coastal lagoon of Mellah (northeast Algeria). These areas (hereafter Shore and Center ) are representative of two different environments typically found in coastal lagoons. The Shore (water depth of about 1.5–2 m) is characterized by relatively higher hydrodynamics, sand to silty-sand sediments and the presence of vegetation ( Ruppia maritima ), the Center (water depth of about 3–3.5 m) is characterized by mud to sandy-mud, organic-enriched sediments due to fine particle accumulation. Results showed two distinct patterns of seasonal variation in Shore and Center assemblages for two consecutive years. In Shore , species richness ( S ), total abundance ( N ) and the abundance of several dominant taxa were highest in summer and/or autumn. This pattern can be related to the local environmental conditions maintaining relatively well oxidized conditions, while increasing food availability, and favoring the recruitment of species and individuals in summer/autumn. On the contrary in Center , S was lowest in summer and autumn, and N and the abundance of fewer dominant taxa were lowest in summer. In Center , the bivalve Loripes lucinalis showed a 10-fold increase from summer to autumn in both years, likely related to the lagoon's hydrodynamics favoring larval transport and settlement in the central sector of the lagoon. Overall, the seasonal variation found in Center followed a regression/recovery pattern typical of opportunistic assemblages occurring in confined organic-enriched environments. In conclusion, our results provide new insight into the patterns of seasonal variation in lagoon soft-sediment benthos and highlight the importance of local environmental conditions on this variation. This study provides a valuable tool for adopting appropriate monitoring strategies in these systems, with special reference to Southern-Eastern Mediterranean lagoons which are expected to suffer from increasing coastal development and human pressure in the near future. [ABSTRACT FROM AUTHOR]