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Cyanobacteria can form nuisance proliferations and produce large concentrations of toxins that pose a health hazard. This thesis investigates cyanotoxin production by New Zealand benthic cyanobacteria. Cyanobacteria were sampled from lakes, reservoirs, streams, and rivers. Thirty-five strains were isolated into culture and screened for genes involved in the biosynthesis of common cyanotoxins. Positive results were confirmed and cyanotoxin concentrations quantified using analytical chemistry techniques. Genes involved in anatoxin a/homoanatoxin a biosynthesis were detected in nine out of ten Phormidium cf. uncinatum strains isolated from a single mat. Anatoxin a was confirmed in these strains by LC–MS/MS at concentrations from 0.3 to 6.4 mg kg⁻¹. One strain also produced homoanatoxin-a. Anatoxin-a variation between strains may explain the wide range in anatoxin a concentrations previously observed in New Zealand. The sxtA gene involved in saxitoxin biosynthesis was identified in Scytonema cf. crispum strains. Saxitoxin was confirmed in strains and environmental samples by Jellett PSP Rapid Test and HPLC–FD. Gonyautoxins, neosaxitoxin, and decarbamoyl derivatives were also detected. This study is the first identification of these compounds in Scytonema and in New Zealand cyanobacterial strains. These strains were isolated from recreational and pre-treatment drinking water reservoirs, highlighting the risk benthic cyanobacteria pose to human and animal health. Experiments were undertaken using cultures of Phormidium and Scytonema to determine how growth influences cyanotoxin production. The effects of iron and copper stress on P. autumnale were also investigated. High iron concentrations disrupted attachment mechanisms. Iron and copper had a significant effect on growth, without significantly affecting anatoxin a production. However, the maximum anatoxin a quota was consistently observed during early exponential growth. Scytonema cf. crispum produced higher saxitoxin quota throughout exponential growth than during the stationary phase. Both the Phormidium and Scytonema growth experiments indicate that high toxin quota can be expected early in benthic mat development, making early detection of these proliferations important.