The hierarchy of factors that control the growth and biomass of Spirogyra sp. was examined for an 18-km reach of the Daly River in the wet/dry tropics of northern Australia. On an annual temporal scale, hydrological disturbances control Spirogyra. Over the wet season (typically December–April), frequent runoff events prevent the colonisation and growth of Spirogyra in the Daly River. This is followed, however, by a lengthy period (typically May–November) without hydrological disturbances and river velocities that favour benthic algal growth. In 2001, Spirogyra became visible in mid-May, then grew to reach a maximum biomass in early August of 28 mg m^-2 of chlorophyll a. The standing crop of Spirogyra was primarily determined by the availability of gravel substrate and the velocity and shear stress at the river-bed. Photosynthetically available radiation (200–800 μE m^-2 s^-1) reaching the river-bed should not have limited algal growth, though self shading within the Spirogyra mats may have been important. Although the growth rate of Spirogyra was probably limited by nutrients, the maximum biomass was constrained by autogenic sloughing. The biomass of Spirogyra steadily declined to half its maximum in early October despite favourable river velocities, most likely a result of nutrient limitation. Spirogyra was then removed from the river by the first major runoff event of the wet season in late October. The hierarchy of factors that control benthic algal biomass in the Daly River are the same as in lower latitudes, though the long period of favourable river velocities when smaller scale, proximate factors (e.g. nutrients, shear stress) control biomass should be noted.