Tropical macroalgal fields are important nurseries for fish of commercial and conservation significance. We investigated how local-scale variations in macroalgal habitat quality interact with large-scale climatic conditions (Southern Oscillation Index, SOI) to influence the recruitment of three emperor species (Lethrinus spp.) at Ningaloo. Fish recruits (<5cm TL) and juveniles (5-15 cm TL) of all three species were almost exclusively found in macroalgal habitats, while adults of two of these species (L. nebulosus and L. atkinsoni) were predominantly found on adjacent coral reefs. Annual supply rates of recruits was positively correlated with variation in the SOI (r2 =0.9), La Nina conditions associated with higher recruitment. However, local rates of recruitment were generally poor predictors of older juvenile abundance. Instead, local juvenile abundance was more closely related to structural characteristics of macroalgae nursery habitat quality (density, canopy height, canopy cover) and/or predator biomass, at the time of survey, with species-specific habitat associations apparent. Thus large scale climate and oceanic processes strongly influence the supply of recruits to Ningaloo, however distribution and persistence of juveniles is more closely related to the structure of local macroalgal patches. These results highlight the importance of macroalgal nursery habitats that maintain high canopy density, height and cover for supporting fish populations.