Ocean acidification (OA) has the potential to affect both calcifying and non-calcifying marine phytoplankton in ways that are only partly understood, but there is even less knowledge about how it may alter the coupling to secondary producers. We investigated the effects of OA on phytoplankton primary production, and its trophic transfer to zooplankton, in a subtropical, eutrophicated coastal water (Wuyuan Bay, China, 24.52^oN, 117.18^oE) using 30 L microcosms. Present day pCO₂ levels (400 µatm) and projected end-of-century concentrations (1000 µatm) were tested in a 7 day bloom experiment. Net primary production was unaffected by OA, although OA did lead to small decreases in cellular growth rates. OA had no measurable effect on micro-/mesozooplankton grazing rates, suggesting it has little impact on the trophic transfer of energy, at least over the short term. Elevated pCO₂ had no effect on phytoplankton nutritional fatty acids (FA) concentrations during the exponential growth phase, but saturated fatty acids (SFA) increased relative to the control during the declining phase on the bloom. The FA profiles of mesozooplankton differed significantly from that of phytoplankton, and this status was not affected by elevated pCO₂ conditions. Our findings show that short-term exposure of plankton communities in eutrophied subtropical waters to projected end-of-century ocean acidification conditions has little effect on primary productivity and the trophic linkage to mesozooplankton.