Phytoplankton and benthic microalgae are critical to the ecosystem productivity of Moreton Bay. The Bay is oligotrophic for most of the year, with acute nutrient pulses delivered by high rainfall events. These nutrient pulses are important drivers of primary production leading to phytoplankton growth and shifts in species composition. Consistent with many coastal areas of the world, the phytoplankton community is dominated by diatoms and a range of pico- and nanoplankton. A west to east gradient of phytoplankton standing stocks across the Bay reflects the influence of river and groundwater discharges. In the past, sewage discharge has also been a significant driver of phytoplankton growth in the western region of the Bay, particularly prior to 2000 when a sewage treatment plant at the mouth of the Brisbane River was upgraded to reduce nutrient discharges. The management of sewage successfully reduced phytoplankton standing stocks, and appears to have improved resilience to acute rainfall events. Acute rainfall events also deliver pulses of sediments, particularly from catchments cleared of vegetation, which affects Moreton Bay light conditions in the water column and silt content of the sediments. The species composition of benthic microalgae (BMA) in the Bay is dominated by diatoms and is driven by the silt content of the sediment. It is hypothesised that low light conditions limit benthic algae and phytoplankton productivity during and following events, in the same way that light limitation affects seagrass productivity; however, research in this area is limited. The exception to diatom dominance in the shallow sediments is in locations where the toxic benthic cyanobacterium Lyngbya majuscula occurs. L. majuscula blooms have become regular in occurrence, especially in the north western Bay. Anthropogenic influences including changes in nutrient inputs likely led to these increased occurrences. Overall the phytoplankton and BMA biomass and species composition of the Bay reflect a relatively healthy system that has improved in response to management intervention. Despite this, persistent chronic pressure from catchment-derived sediment and nutrients has potential to erode this resilience.