Crown-of-thorns starfish (COTS) outbreaks cause widespread coral mortality across the Great Barrier Reef. When COTS larvae are in the plankton, nutrient rich coastal runoff simultaneously generates phytoplankton blooms, which potentially enhances their food levels and success to precipitate an outbreak, and lowers salinity. The potentially deleterious effects of decreased salinity on COTS larvae has not been considered. The impact of decreased salinity and increased food on COTS bipinnaria larvae was investigated. The percentages of larval normal morphology and larval survival were determined in response to 7 salinities and 3 algal food density treatments, at four time points. Salinity performance curves showed that salinity was the major factor determining larval performance. At 24 h the optimal salinity (Sopt) (≥ 90 % larval survival) was ~26–34 ‰ and the salinity with 50 % mortality (LS50) was 21.62 ‰. By 96 days the LS50 had increased to 24.57 ‰, showing a narrowing of salinity tolerance over time. Salinities for the sharp onset of deleterious effects approximated ~22–25 ‰. These are levels that larvae would experience in a runoff plume. Counter to the paradigm of enhanced larval success, these findings indicate a negative effect of runoff for COTS larvae.