While standard methods for chlorine taste and odor (T&O) detection and rejection thresholds exist, little rigorous research has been conducted on T&O thresholds in humanitarian settings. To fill this gap, we estimated chlorine T&O detection and rejection thresholds using the Forced-Choice Triangle Test (FCT) and Flavor Rating Assessment (FRA) standard methods in a Ugandan refugee settlement. We conducted these tests with 410 male and female participants, aged 5–72 years, using piped and trucked surface water and bottled water. We also conducted 30 focus group discussions and 37 surveys with data collectors. Median chlorine detection thresholds were 0.56, 1.40, and 1.67 mg/L, for piped, trucked, and bottled water, respectively. Rejection was calculated using ratings (as per the method) and five different previously-used thresholds, and was 1.6, 2.0, and 1.6 mg/L (ratings) and 2.19, 1.85, and 1.67 mg/L (using the FCT threshold method with FRA data) for piped, trucked, and bottled water, respectively. Detection and rejection thresholds were significantly associated with water quality (including turbidity, pH, electrical conductivity, and temperature), participant age and education. We observed high intra- and inter-individual variability, which decreased with participant experience. We found the method used to calculate rejection thresholds influenced results, highlighting the need for a standard method to analyze FRA data. Data collectors and participants recommended shortening protocols and evaluating fewer concentrations, and highlighted difficulties in creating accurate FRC concentrations for testing. This study provides insights on using standard methods to assess T&O thresholds in untrained populations, and results are being used to develop rapid field T&O protocols for humanitarian settings.