Seagrass meadows are a critical component of estuarine and coastal seascapes, and their structure influences fish assemblages at multiple spatial scales. The patch mosaic model, which defines the seascape as a collection of interacting habitat types, is increasingly adopted to prioritise protected areas and design ecological restoration schemes, hence helping to preserve seagrass meadows and the associated fish assemblages. Despite that, there are few studies investigating the relative contribution of environmental characteristics measured at different spatial scales in determining the distribution of seagrass fish. This study collects fish and environmental observations taken at both site and seascape scales in seagrass meadows in the Venice lagoon (Adriatic Sea, Italy). By means of generalised linear models, it aims to disentangle the relative influence of local water quality and habitat characteristics from that of habitat mosaic properties, investigating the response of whole fish assemblage descriptors, feeding guilds and dominant species. While confirming the primary importance of local habitat quality, the study highlights that also seagrass habitat structure at the seascape scale is relevant for seagrass fish assemblages, influencing total biomass, biomass of macrobenthivorous and hyperbenthivorous/piscivorous species and seagrass specialists such as syngnathids. Conservation of seagrass fish assemblages can therefore be promoted in Mediterranean coastal lagoons by preserving or restoring some features of the habitat mosaic, namely the extension of seagrass patches and their shape complexity, in addition to local water quality and seagrass cover.