Global warming (and the consequent increase in sea surface temperature) is expected to modify rates of gross primary production (GPP), respiration ( R ), and net calcium carbonate (CaCO 3 ) dissolution in permeable coral reef carbonate sediments. Previous simulations of seawater warming on coral reef sediments found a decline in the GPP/ R ratio and an associated increase in CaCO 3 dissolution but were only conducted over a short timescale (< 24 h). To date, no studies have examined the prolonged (> 24 h) effect of seawater warming on coral reef CaCO 3 sediment metabolism and dissolution, which may allow the benthic community to acclimatise. This study used 600-L flume aquaria to examine the effect of seawater warming on GPP, R , and CaCO 3 dissolution in the permeable coral reef CaCO 3 sediments of Mo’orea, French Polynesia, over a period of 15 d. On average, when exposed to warmed seawater (+ 2.8 °C), R in the CaCO 3 sediments was enhanced (+ 58%) to a greater extent than GPP (+19%), resulting in a decline in GPP/ R (− 23%) and an associated increase in net CaCO 3 dissolution (+ 126%). The magnitude of these warming-mediated metabolic changes increased each day until reaching a plateau after about 8 d, indicating that 24-h experiments may be underestimating the effect of warming over longer timescales. Interestingly, the increase in dissolution relative to control treatments was more striking during the day (+ 163%) than at night (+ 89%), suggesting that warming acted to both enhance geochemical dissolution and reduce biogenic calcification or inorganic precipitation. Together, these data indicate that, over the timescale observed here, photosynthesis and associated inorganic and biogenic CaCO 3 precipitation do not exhibit the ability to counterbalance the warming-mediated increase in sediment heterotrophy and CaCO 3 dissolution.