Bycatch remains the single greatest threat to cetaceans globally. Within Australia, the Queensland Shark Control Program (QSCP) has operated since 1962, deploying shark nets and drumlines along the coast to increase bather safety and reduce shark attack risk. Despite this, incidental capture of cetaceans, including threatened inshore dolphins and migrating whales has remained a significant and under-addressed issue. Using linear regression and generalised additive mixed models, we assessed >60 years of data to identify the spatio-temporal, ecological, and operational factors driving cetacean bycatch. Cetacean (by)catch per unit effort (CPUE) significantly increased over time, with seasonal effects evident (higher in autumn/winter for odontocetes and winter/spring for mysticetes). Southern Queensland had significantly higher bycatch than both the central and northern zones, while nets were more likely to entangle cetaceans than drumlines. Smaller individuals (juvenile) were most vulnerable to capture in QSCP. Our analysis highlighted the importance of sea surface temperature (SST), meridional ocean velocity (VCUR), wind speed anomaly, moon phase, Southern Oscillation Index (SOI), sea level anomaly, salinity, and chlorophyll as significant predictors of cetacean bycatch. However, the relative influences of these factors varied depending on suborder. Odontocetes had higher CPUE with lower SST, lower wind speeds, negative VCUR (southward water flow), and greater periods of new and full moon days. Mysticetes also exhibited higher CPUE with colder SST and greater periods of new and full moon days, but experienced higher bycatch during La Niña seasons (positive SOI), higher salinity, higher chlorophyll, and larger sea level anomalies (i.e., a stronger and closer East Australian Current). These findings demonstrate that predictable and measurable spatio-temporal, operational, and environmental variables shape the occurrence of cetacean bycatch in QSCP, providing a basis to inform management strategies for minimising non-target mortality in coastal fisheries and reinforcing the value of long-term ecological monitoring for adaptive conservation management.