The bioavailability of organic matter (OM) was assessed at three locations during the dry and wet seasons in the Great Barrier Reef (GBR), by measuring changes in particulate organic matter (POM) and dissolved organic matter (DOM) concentrations during laboratory incubations over 50 d. The sites did not show any difference in salinity and, therefore, observed changes could be related to factors such as disparities in the biological activity and/or the impact of sediment resuspension rather than to location. Our results demonstrate that the POM pool has a higher bioavailability than the DOM pool, with the C, N, and P‐containing compounds being more bioavailable than the C and N‐containing molecules, which in turn are more labile than compounds containing just C. The addition of labile POM to the DOM pool did not impact the bioavailability of DOM, suggesting that priming had no major impact on the degradation of this pool in these experiments. Furthermore, our results demonstrate that 94% and 75% of the bioavailable N and P are contained in the organic fraction delivering enough nutrients to sustain phytoplankton productivity in the GBR. Using the obtained degradation rate constants and an average water residence time of 2 weeks, we show that most bioavailable POM (> 96%) and DOM (> 83%) is degraded before reaching the outer shelf. Our results emphasize that OM is a key and mostly unaccounted part of the C, N, and P cycles in tropical coastal waters of the GBR.