Fisheries are a staple human activity supported by coastal lagoons. Together with water quality and trophic status, lagoon morphology is acknowledged as one of the main ecological drivers of fishery yields; however, the role of lagoon seascape structure is still poorly understood. This paper investigates how morphological variables, habitat distribution and seascape diversity and complexity affect yields of artisanal fishery performed with fyke nets in the Venice Lagoon (northern Adriatic Sea, Italy). Two spatial scales were considered in the analysis, with water quality parameters (temperature, salinity, dissolved oxygen, turbidity, water residence times, N, P and chlorophyll-a concentrations) being measured at a fine, fyke-net scale and morphological (average bottom elevation and sediment grain size) and habitat features (habitat proportion, diversity and complexity) being measured at a broader, seascape scale. Generalised linear mixed models were employed to model 8 years of nekton and green crab catches, disentangling the role of broad-scale morphology and seascape from that of fine-scale water quality. Broad-scale variables clearly influenced fishery target species. Among them, lagoon residents were associated with specific morphological and habitat characteristics, while marine migrants showed a stronger link with overall habitat diversity and complexity. This evidence emphasises how artisanal fishery in the Venice Lagoon relies on the conservation of morphological and habitat heterogeneity. Moreover, it highlights how habitat restoration performed at the seascape level should also be taken into account, in addition to controlling hydrology and water quality, when managing fishery resources in coastal lagoons.