Microalgal blooms are one of the most visible responses to anthropogenic nutrient loadings in coastal ecosystems. However, differentiating sources of nutrients causing blooms remains a challenge. The response of phytoplankton and benthic microalgae (BMA) to nutrient loads was compared across tidal creeks with and without secondary treated sewage in a tropical estuary. Concentrations of the sewage marker, coprostanol, were higher near sewage discharge points and decreased downstream. This was commensurate with a decline in nitrogen and phosphorus concentrations suggesting that sewage was the main source of nitrogen and phosphorus. Primary productivity in the water column was limited by nitrogen availability in absence of sewage, with nitrogen saturation in the presence of sewage. Phytoplankton primary productivity rates and chlorophyll a concentrations increased in response to sewage, and there was a greater response than for BMA. There was no evidence of a change in algal pigment proportions within the phytoplankton or BMA communities. This study highlights the scale and type of response of algal communities to sewage nutrients in situ.