Existing studies indicate that multiple physical habitat characteristics can affect the abundance and distribution of larval stream salamanders. We quantified seasonal patterns of microhabitat use by larval southern two-lined salamanders (Eurycea cirrigera) and microhabitat availability in two Georgia Piedmont streams from April 2000 to April 2001. Larvae were generally significantly underrepresented in deep areas with low percentages of coarse substratum, locations dominated by bedrock substrata, and areas lacking debris (November sample only). Both between-stream differences in microhabitat use and within-stream seasonal differences in microhabitat use generally reflected differences in microhabitat availability. The close association of larval two-lined salamanders with substrata that provided cover indicates that habitat heterogeneity is important for this species. Consequently, loss of habitat complexity through anthropogenic disturbance may result in decreases in abundance of southern two-lined salamanders in Georgia.