Big and Cowarts creeks lie in extreme southeastern Alabama and form the headwaters of Chipola River. Qualitative and quantitative sampling for freshwater mussels in these reaches during 2006 and 2007 revealed an intact fauna, relative to historical reports. A cumulative total of 17 species, including federally protected Elliptio chipolaensis (Chipola Slabshell), Lampsilis subangulata (Shinyrayed Pocketbook), Medionidus penicillatus (Gulf Moccasinshell), and Pleurobema pyriforme (Oval Pigtoe), was encountered. A total of 3382 mussels (density 5.84 per m2) was estimated for one 65-m reach of Big Creek and 9627 mussels (density 8.09 per m2) were estimated to occur in one 170-m reach of Cowarts Creek. Tributaries had depauperate faunas, apparently due to substrate instability.