To satisfy the requirements of the Filtration Avoidance Determination and to collect data needed to make future decisions, the New York City Department of Environmental Protection (DEP) conducted a disinfection study for the Catskill and Delaware water systems. This paper presents the results of the disinfection study conducted to investigate primary disinfection without subsequent filtration to satisfy current Surface Water Treatment Rule (SWTR) regulations and to achieve increased inactivation levels for Cryptosporidium. Several disinfectants (ozone, chlorine, and chlorine dioxide) and sequential application of disinfectants (ozone followed by chlorine) were studied to meet three inactivation levels at various temperature conditions. These inactivation levels were defined as a high CT goal of 2-log Cryptosporidium inactivation, a mid CT goal of 1-log Cryptosporidium inactivation, and a low CT goal of 3-log Giardia or 4-log virus inactivation. The CT goals were satisfied for all three conditions established (low CT, mid CT, and high CT) with reasonable chlorine dioxide and ozone doses and contact times. Chlorine disinfection and sequential disinfection (ozone followed by chlorine) were not effective in meeting the established CT goals for the initial doses and contact times selected.