In this paper, the dynamics of primary production in the Daly River in tropical Australia are investigated. We used the diurnal-curve method for both oxygen and pH to calculate photosynthesis and respiration rates as indicators of whole-river productivity. The Daly River has maximum discharges during the summer, monsoonal season. Flow during the dry season is maintained by groundwater discharge via springs. The study investigated how primary production and respiration evolve during the period of low flow in the river (April–November). The relationship between primary production and the availability of light and nutrients enabled the role of these factors to be assessed in a clear, oligotrophic tropical river. The measured rate of photosynthesis was broadly consistent with the estimated mass of chlorophyll associated with the main primary producers in the river (phytoplankton, epibenthic algae, macroalgae, macrophytes). A significant result of the analysis is that during the time that plant biomass re-established after recession of the flows, net primary production proved to be ~4% of the rate of photosynthesis. This result and the observed low-nutrient concentrations in the river suggest a tight coupling between photosynthetic fixation of carbon and the microbial degradation of photosynthetic products comprising plant material and exudates.