The efficiency of light used for photosynthesis, when standardised for areal chlorophyll (Chl)-a biomass, is summarised by the light utilisation efficiency parameter and is dependent on light at the water’s surface, the underwater light climate and autotroph characteristics. Herein we examined the relationships between light, photosynthesis, respiration and autotroph biomass in a tropical savanna river in northern Australia during the dry season when autotroph biomass accumulated following wet season disturbance. The river’s autotrophs comprised mainly benthic microalgae, macroalgae and macrophytes. Total Chl-a and dry weight biomasses increased 4- and 27-fold respectively over 5 months, whereas photosynthesis doubled. Photosynthesis was light limited and, when standardised for Chl-a and dry weight biomasses, declined with increasing biomass, despite increasing incident light through the study period. We surmised this was due to self-shading and autotrophic composition, which had variable Chl-a content and resulted in a 10-fold reduction in the light utilisation efficiency with increasing light and biomass. Because respiration was tightly coupled to photosynthesis, biomass-standardised respiration also decreased with increasing biomass. Autotrophic self-shading and composition can have significant effects on light utilisation efficiency and the biomass–photosynthesis relationship, and warrant consideration when interpreting photosynthesis for river health monitoring.