A number of marine microalgae are known to produce toxins that can accumulate in shellfish and when eaten, lead to toxic and potentially fatal reactions in humans. This paper reports on the occurrence and seasonal variations of algal toxins in the waters, phytoplankton and shellfish of Southeast Queensland, Australia. These algal toxins include okadaic acid (OA), domoic acid (DA), gymnodimine (GD), pectenotoxin-2 (PTX-2) and pectenotoxin-2-seco acid (PTX-2-SA), which were detected in the sampled shellfish and phytoplankton, via HPLC-MS/MS. Dissolved OA, PTX-2 and GD were also detected in the samples collected from the water column. This was the first occasion that DA and GD have been reported in shellfish, phytoplankton and the water column in Queensland waters. Phytoplankton tows contained both the toxic Dinophysis and Pseudo-nitzschia algae species, and are suspected of being the most likely producers of the OA, PTX-2s and DA found in shellfish of this area. The number of cells, however, did not correlate with the amount of toxins present in either shellfish or phytoplankton. This indicates that toxin production by algae varies with time and the species present and that number of cells alone cannot be used as an indicator for the presence of toxins. The presence of OA and PTX-2s were more frequently seen in the summer, while DA and GD were detected throughout the year and without any obvious seasonal patterns.