Micro-ozone, permanganate, ferrate, and chlorine dioxide were applied as pre-oxidants to meet conventional requirements for water quality and algal control. The formation of typical carbonaceous disinfection by-products (C-DBPs) and emerging nitrogenous disinfection by-products (N-DBPs) during both chlorination and chloramination were investigated with combinations of different processes: (i) coagulation-sedimentation-filtration (CSF), (ii) pre-KMnO4/O-3/K2FeO4/ClO2 matched with CSF, and (iii) pre-KMnO4/O-3/K2FeO4/ClO2 coupled with CSF and followed by granular activated carbon (GAC)/O-3-GAC advanced treatment. All conventional water quality indexes met the requirements of the national standards for drinking water quality of China (GB57492006) when the system was under stable operation; only NH4+-N, which only met the requirement with either pre-oxidation or post-ozonation, failed to do so. Micro-ozone pre-treatment coupled with CSF and O3-GAC showed the best performance in removing chloroform (CF) and dichloracetonitrile (DCAN) precursors. Preoxidation had a negative impact on chloropicrin (TCNM) and chloral hydrate formation, but a positive effect on DCAN. The trade-off analysis based on the toxicity of the selected DBPs indicated that pre-oxidation (KMnO4, O3, K2FeO4, and ClO2) had a positive influence on the control of overall cytotoxicity, and O3 pre-oxidation coupled with CSF followed by O-3-GAC performed the best. However, for the control of overall genotoxicity, the ClO2 pretreatment showed best results, whether or not GAC or O-3-GAC was involved. These results are important for optimizing the design of the treatment processes in drinking water treatment plants using eutrophic lake water where precursors for regulated C-DBP and unregulated N-DBP formation are prevalent.