The understanding of microbial susceptibility to disinfectants is an important step to provide drinking water (DW) of adequate microbiological quality. In drinking water distribution systems (DWDS) the application of disinfectants is the main approach to control microorganisms. Although chlorine has been commonly used for DW treatment, the increase of microbial resistance and the production of harmful disinfection by-products promote the necessity to seek new alternatives. This study evaluated the antimicrobial activity of sodium dichloroisocyanurate (NaDCC), trichloroisocyanuric acid (TCCA), and pentapotassium bis(peroxymonosulphate) bis(sulphate) (OXONE) against two emerging pathogens isolated from DW, Acinetobacter calcoaceticus and Stenotrophomonas maltophilia. Free chlorine from calcium hypochlorite was used for comparison. The dose and time-responses against planktonic bacteria were performed as well as the assessment of the effects on membrane integrity. Moreover, the effects against 48 h-old biofilms formed on polyvinyl chloride and stainless steel were evaluated in terms of biofilm culturability and removal. Minimum bactericidal concentrations of 2.1 and 3.1 mg/L for NaDCC, 2.5 and 3.8 mg/L for TCCA, 340 and 690 mg/L for OXONE, and 0.80 and 1.0 mg/L for free chlorine alone were obtained against S. maltophilia and A. calcoaceticus, respectively. The kinetic modeling revealed that NaDCC and TCCA caused similar inactivation rates and the time for first log reduction by OXONE was less than 10 min, for both bacteria. All the disinfectants triggered significant bacterial cytoplasmic membrane destabilization, even at sub-lethal concentrations. A 30 min treatment with the disinfectants allowed a reduction in the biofilm culturability up to 5 log. OXONE was the disinfectant with the best efficiency against both bacterial biofilms. However, none of the disinfectants caused significant biofilm removal (reduction < 1 log cells/cm2). This study highlights NaDCC, TCCA, and OXONE as promising alternatives to free chlorine for DW disinfection, particularly for planktonic growth control and biofilm culturability reduction.