Vernal pools are sensitive environments that provide critical habitat for many species, including amphibians. These small water bodies are not always protected by pesticide label requirements for no-spray buffer zones, and the occurrence of pesticides in them is poorly documented. In this study, we investigated the occurrence of glyphosate, its primary degradation product aminomethylphosphonic acid, and additional pesticides in vernal pools and adjacent flowing waters. Most sampling sites were chosen to be in areas where glyphosate was being used either in production agriculture or for nonindigenous plant control. The four site locations were in otherwise protected areas (e.g., in a National Park). When possible, water samples were collected both before and after glyphosate application in 2005 and 2006. Twenty-eight pesticides or pesticide degradation products were detected in the study, and as many as 11 were identified in individual samples. Atrazine was detected most frequently and concentrations exceeded the freshwater aquatic life standard of 1.8 micrograms per liter (μg/l) in samples from Rands Ditch and Browns Ditch in DeSoto National Wildlife Refuge. Glyphosate was measured at the highest concentration (328 μg/l) in a sample from Riley Spring Pond in Rock Creek National Park. This concentration exceeded the freshwater aquatic life standard for glyphosate of 65 μg/l. Aminomethylphosphonic acid, triclopyr, and nicosulfuron also were detected at concentrations greater than 3.0 μg/l.