Within low-nutrient tropical oceans, islands and atolls with higher primary production support higher fish biomass and reef organism abundance. External energy subsidies can be delivered onto reefs via a range of physical mechanisms. However, the influence of spatial variation in primary production on reef fish growth and condition is largely unknown. It is not yet clear how energy subsidies interact with reef depth and slope. Here we test the hypothesis that with increased proximity to deep-water oceanic nutrient sources, or at sites with shallower reef slopes, parameters of fish growth and condition will be higher. Contrary to expectations, we found no association between fish growth rate and sites with higher mean chlorophyll-a values. There were no differences in fish δ15N or δ13C values between depths. The relationship between fish condition and primary production was influenced by depth, driven by increased fish condition at shallow depths within a primary production ‘hotspot’ site. Carbon δ13C was depleted with increasing primary production, and interacted with reef slope. Our results indicate that variable primary production did not influence growth rates in planktivorous Chromis fieldi within 10–17.5 m depth, but show site-specific variation in reef physical characteristics influencing fish carbon isotopic composition.