Toilets contaminated with infectious organisms are a recognized contact disease transmission hazard. Previous studies indicate that toilet bowl water can remain contaminated for several flushes after the contamination occurs. This study characterized contamination persistence over an extended series of flushes using both indicator particles and viable bacteria. For this study, toilets were seeded with microbe-size microbial surrogates and with Pseudomonas fluorescens or Clostridium difficile bacteria and flushed up to 24 times. Bowl water samples collected after seeding and after each flush indicated the clearance per flush and residual bowl water contaminant concentration. Toilets exhibited 3 + log10 contaminant reductions with the first flush, only 1–2 logs with the second flush, and less than 1 log thereafter. Contamination still was present 24 flushes postcontamination. Clearance was modeled accurately by a two-stage exponential decay process. This study shows that toilet bowl water will remain contaminated many flushes after initial contamination, posing a risk of recurring environmental contamination and associated infection incidence.