Something that's contaminated is polluted or fouled. People should not drink or brush their teeth with contaminated water.
If a medical test or sample becomes contaminated, it means that some foreign material has corrupted it — the test has to be retaken. Likewise, if the water in your well is contaminated with arsenic, which is poisonous in high enough concentrations, you'll have to drain and clean the well or possibly even dig a new one. Things become contaminated when they're exposed to dangerous or dirty substances. The Latin root of contaminated is contaminare, "to defile."