Estimates of primary productivity in aquatic ecosystems are commonly based on variation in (Figure presented.), rather than (Figure presented.). The photosynthetic quotient (PQ) is used to convert primary production estimates from units of (Figure presented.) to C. However, there is a mismatch between the theory and application of the PQ. Aquatic ecologists use PQ = 1–1.4. Meanwhile, PQ estimates from the literature support PQ = 0.1–4.2. Here, we describe the theory on why PQ may vary in aquatic ecosystems. We synthesize the current understanding of how processes such as (Figure presented.) assimilation and photorespiration can affect the PQ. We test these ideas with a case study of the Clark Fork River, Montana, where theory predicts that PQ could vary in space and time due to variation in environmental conditions. Finally, we highlight research needs to improve our understanding of the PQ. We suggest departing from fixed PQ values and instead use literature-based sensitivity analyses to infer C dynamics from primary production estimated using (Figure presented.).