At a paper manufacturing mill (PML) that had been previously part of an integrated pulp (bisulphite) and paper mills industry, cyanobacterial blooms were observed in the mill’s aerated stabilization basin (ASB) ponds at about 3 years after pulping had been discontinued. This study aimed to determine the factors that led to bloom occurrences and potential control strategies applicable to the paper manufacturing mill’s, aerated stabilization basin system that discharges wastewaters into a coastal lake. Following discontinuation of pulping, the colour of the wastewaters reduced to low levels (~ 10 Hazen units or less), while the levels of nutrient remained potentially supportive of cyanobacteria growth with total phosphorus at ~ 0.1 mg/L and total nitrogen at > 2.5 mg/L. Incidences of blooms in the ABS were associated with preceding average monthly rainfalls and wind speeds being less (~ 44% and ~ 7%, respectively) and average direct sunlight hours being greater (~ 9%) than the long-term average values. Zinc was investigated for control of cyanobacteria as this metal is less toxic to aquatic organisms and microflora than copper algaecides. In laboratory culture trials, zinc was found to inhibit growth of M. aeruginosa (strain MIC338) and Pseudanabaena sp. when dosed at ~ 2.5 mg/L. The inhibition of cyanobacteria by zinc was found to vary between ASB pond samples which had different in situ chlorophyll a levels. This study found that the PML wastewaters investigated can be supportive of cyanobacterial growth to bloom levels after discontinuation of pulping processes and that zinc has potential as a cyanobacteria control agent.