Harmful algal blooms (HABs) have wide-ranging environmental impacts, including on aquatic species of social and commercial importance. In New Zealand (NZ), strategic growth of the aquaculture industry could be adversely affected by the occurrence of HABs. This review examines HAB species which are known to bloom both globally and in NZ and their effects on commercially important shellfish and fish species. Blooms of Karenia spp. have frequently been associated with mortalities of both fish and shellfish in NZ and the sub-lethal effects of other genera, notably Alexandrium spp., on shellfish (which includes paralysis, a lack of byssus production, and reduced growth) are also of concern. Climate change and anthropogenic impacts may alter HAB population structure and dynamics, as well as the physiological responses of fish and shellfish, potentially further compromising aquatic species. Those HAB species which have been detected in NZ and have the potential to bloom and harm marine life in the future are also discussed. The use of environmental DNA (eDNA) and relevant bioassays are practical tools which enable early detection of novel, problem HAB species and rapid toxin/HAB screening, and new data from HAB monitoring of aquaculture production sites using eDNA are presented. As aquaculture grows to supply a sizable proportion of the world’s protein, the effects of HABs in reducing productivity is of increasing significance. Research into the multiple stressor effects of climate change and HABs on cultured species and using local, recent, HAB strains is needed to accurately assess effects and inform stock management strategies.

Temporal changes in the abundance and horizontal and vertical distribution of phytoplankton biomass (chlorophyll a) in Tasman Bay, New Zealand were associated with changes in water column stratification, because of seasonal climatic effects and variations in the magnitude of freshwater inflows. The water column throughout the bay was usually strongly stratified. Vertical gradients in salinity, the result of outwelling river plumes overlying deeper more saline waters, usually played the major role in stabilising the water column. However, during summer low river‐flow periods, temperature stratification was also important. A persistent east to west gradient in Simpson's potential energy anomaly (an index of the strength of stratification) existed across the bay at most times, because of the dominant influence of the Motueka River plume. From late spring to late summer most of the nutrient depleted euphotic zone contained low chlorophyll a (Chl. a) concentrations while below the base of the pycnocline, turbid water containing re‐suspended sediments and relatively high Chl. a levels persisted. It is debatable, given the susceptibility of scallops to high levels of suspended silt, whether this condition is beneficial to these commercially important bivalves. Diatom blooms in autumn and spring, representing the annual productivity maxima, occurred when the water column beyond the extent of the Motueka River plume became well mixed. At this time the conditions for shellfish nutrition are probably at their best. At most other times flagellate‐dominated phytoplankton communities within subsurface concentrated Chl. a layers were associated with a mid water column (10–15 m), bay‐wide, pycnocline. This is a common feature of the structure of the water column of Tasman Bay that coincides with the depth range within which scallop growth and survival is highest and mussel nutrition and spat catching is probably optimal. Aquaculture management options and strategies for fisheries enhancement may be developed using these data such as the timing and depth of installation of bivalve spat catching gear to optimise shellfish nutrition and successful spat falls. The future lies in the installation of real‐time monitoring equipment within the bay and development of adaptive phytoplankton productivity models based on hydrodynamic models of water column circulation and vertical structure.

Blooms of the dinoflagellate Dinophysis acuminata occur every year in an important mussel cultivation area in Port Underwood, Marlborough Sounds, New Zealand. Annual maximum cell numbers range from 1500–75,000 cells L⁻¹ and over 25 years of weekly monitoring the D. acuminata bloom has never failed to exhibit peaks in abundance at some time between spring and autumn. During winter (June–August) the dinoflagellate is often undetectable, or at low levels (≤100 cells L⁻¹), and the risk of diarrhetic shellfish poisoning (DSP)-toxin contamination over this period is negligible. Bloom occurrence may be coupled to the abundance of D. acuminata prey (Mesodinium sp.) but the mechanism by which it maintains its long-term residence in this hydrologically dynamic environment is unknown. The toxin profile of D. acuminata is dominated by pectenotoxin-2 (PTX-2) and dinophysistoxin-1 (DTX-1), but the cellular toxin content is low. It is rare that free DTX-1 is detected in mussels as this is invariably exclusively present as fatty acid-esters. In only five out of >2500 mussel samples over 16 years have the levels of total DTX-1 marginally exceeded the regulated level of 0.16 mg kg⁻¹. It is also rare that free PTX-2 is detected in mussels, as it is generally only present in its hydrolysed non-toxic PTX-2 seco acid form. The D. acuminata alert level of 1000 cells L⁻¹ is often exceeded without DTX-1 residues increasing appreciably, and this level is considered too conservative.