Alkyldimethylbenzylammonium chlorides (ADBACs), classified as second-generation quaternary ammonium compounds, are extensively employed across various sectors, encompassing veterinary medicine, food production, pharmaceuticals, cosmetics, ophthalmology, and agriculture. Consequently, significant volumes of ADBAC C12-C16 are discharged into the environment, posing a threat to aquatic organisms. Regrettably, comprehensive data regarding the toxicological characteristics of these compounds remain scarce. This research aimed to determine whether or not ADBAC C12-C16, at environmentally relevant concentrations (0.4, 0.8, and 1.6 μg/L), may instigate oxidative stress and alter the expression of apoptosis-related genes in the liver, brain, gut, and gills of Danio rerio adults (5-6 months). The findings revealed that ADBAC C12-C16 elicited an oxidative stress response across all examined organs following 96 h of exposure. Nonetheless, the magnitude of this response varied among organs, with the gills exhibiting the highest degree of susceptibility, followed by the gut, liver, and brain, in descending order. Only the gut and gills of the examined organs displayed a concentration-dependent reduction in the activity of superoxide dismutase (SOD) and catalase (CAT). Akin to the oxidative stress response, all organs exhibited a marked increase in bax, blc2, casp3, and p53 expression levels. However, the gills and gut manifested a distinctive suppression in the expression of nrf1 and nrf2. Our Principal Component Analysis (PCA) confirmed that SOD, CAT, nrf1, and nrf2 were negatively correlated to oxidative damage biomarkers and apoptosis-related genes in the gills and gut; meanwhile, in the remaining organs, all biomarkers were extensively correlated. From the above, it can be concluded that ADBAC C12-C16 in low and environmental concentrations may threaten the health of freshwater fish.