Rock lobster species are found worldwide and have a life history that includes development through a planktonic phyllosoma followed by a nektonic non-feeding puerulus that relies on stored energy during recruitment into near-shore habitats. Recruitment to adult populations of western rock lobster (Panulirus cygnus) is highly variable and is likely to be strongly influenced by shelf width and oceanic conditions affecting cross-shelf transport and nutrition. Since the nutritional status of newly settled pueruli will reflect the phyllosoma feeding environment and distance swum, we studied levels of lipid, fatty acid (FA) and protein of 422 pueruli and 79 first instar juveniles from four Western Australian locations. Lipid levels generally were inversely related to shelf width but were variable, suggesting pueruli may travel complex trajectories to coastal settlement. Lipid and FA composition of pueruli were consistent with spatial and seasonal variation in Leeuwin Current and coastal productivity regimes. Seasonal differences in FA composition occurred regardless of the year of settlement. Pueruli had lower lipid levels during ENSO years, when recruitment tends to be lower also. Measures of puerulus nutritional status appear to provide valuable insights into the processes underpinning recruitment in Panulirus cygnus and other commercially and ecologically important species.