1. One of the major challenges to ensure effective restoration of estuarine habitats is to establish success criteria to determine whether the goals of restoration are met. 2. The aim of this work is to propose and test an approach to identify reference conditions and assess the recovery of nekton (fish, decapods and cephalopods) assemblages at seagrass restoration sites. 3. Nekton sampling took place from 2014 to 2017 in the northern Venice lagoon (northern Adriatic Sea, Italy) during spring at eight sites subjected to seagrass (Zostera marina and Zostera noltei) transplantation. In spring 2016, five natural seagrass sites in the same area were additionally sampled, and physico‐chemical water parameters and habitat structure were also recorded. 4. A multivariate generalized linear model approach was adopted in order to disentangle the relative effect of water quality and seagrass habitat structure on nekton assemblages of natural habitats. Models were subsequently employed to predict species composition of nekton fauna at each transplantation site, to identify the reference assemblage expected under site‐specific abiotic and habitat characteristics. 5. The average distance of the observed assemblage from reference conditions was used to track temporal trajectories of nekton colonization at transplantation sites, and to ultimately evaluate the recovery rate towards restoration goals. 6. This study highlights how a predictive approach could serve management purposes in ecological restoration, providing a concise tool to assess the functionality of restored habitats for associated fauna.
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