There are concerns that reefs will transition from net calcifying to net dissolving in the near future due to decreasing calcification and increasing dissolution rates. Here, we present in situ rates of net ecosystem calcification (NEC) and net ecosystem production (NEP) on a coral reef flat using a slack‐water approach. Up until dusk, the reef was net calcifying in most months but shifted to net dissolution in austral summer, coinciding with high respiration rates and a lower aragonite saturation state (Ωarag). The estimated sediment contribution to NEC ranged from 8% to 21% during the day and 45% to 78% at night, indicating that high rates of sediment dissolution may cause the transition to reef dissolution. This late afternoon seasonal transition to negative NEC may be an early warning sign of the reef shifting to a net dissolving state and may be occurring on other reefs. Plain Language Summary Positive rates of net ecosystem calcification and net ecosystem production are regarded as fundamental to the healthy functioning of coral reef ecosystems. In particular, positive ecosystem calcification is required to maintain the structural complexity that sustains many of the ecosystem functions of coral reefs. While most reefs are currently net calcifying, there is growing concern that increased pressures from rising sea surface temperatures and reductions in ocean surface pH (ocean acidification OA) will both depress coral calcification and increase dissolution. This could result in a shift of the whole ecosystem closer to a state of net dissolution before the end of the century. Here, we measured hourly afternoon rates of net ecosystem calcification and production on a coral reef flat over 10 months of the year. We found that the reef flat was already showing signs of net dissolution during certain times of the year (austral summer), which may become more extreme under global climate change. These temporary shifts in coral reef metabolism may provide insight into how the ecosystem will respond to future, more persistent periods of net dissolution driven by OA. Key Points Ecosystem calcification and sediment calcification on Heron Island reef exceed dissolution such that net ecosystem calcification (NEC) remains largely positive Shallow, calcium carbonate sediments contribute 8%–12% of reef NEC during the day and at least 45%–78% of reef NEC at night The seasonal shifts to negative net ecosystem calcification before dusk may be a precursor of periodic net ecosystem dissolution