AbstractEutrophication-driven harmful algal blooms (HABs) can have secondary effects on larval fishes that rely on estuaries as nurseries. However, few studies worldwide have quantified these effects despite the global rise in eutrophication. This study presents a novel approach using biochemical body condition analyses to evaluate the impact of HABs on the growth and body condition of the larvae of an estuarine resident fish. Recurrent phytoplankton blooms ofHeterosigma akashiwooccur in the warm-temperate Sundays Estuary on the southeast coast of South Africa. The response in body condition and assemblage structure on larval estuarine roundherring (Gilchristella aestuaria) was measured in conjunction with bloom conditions, water quality and zooplanktonic prey and predators. Larvae and early juveniles were sampled during varying intensity levels, duration and frequency of hypereutrophic blooms. This study demonstrated that extensive HABs could significantly impact larval roundherring,G. aestuaria, by decreasing larval nutritional condition and limiting their growth, resulting in poor grow-out into the juvenile phase. Poor condition and growth may likely affect recruitment success to adult populations, and sinceG. aestuariais an important forage fish and zooplanktivore, poor recruitment will hold consequences for estuarine food webs.