The low fow analysis for small-mid sized river basins is very difficult because of insufficient flow data or ungauged basins. The objective of this study is to suggest effective method of low flow using area function method for calculating Total Maximum Daily Loads (TMDL) by considering environmental carrying capacity. Two watersheds which are Juchon watershed having $606km^2$ areas and ungauged watershed having $4,551km^2$ areas were selected for this study. As a result of application, the low flow in the downstream of Juchon River and the Han River after confluence of Okdong River were $1.9m^3/s$ and $20.7m^3/s$, respectively. Then we consider the target BOD of 1.0-1.2mg/l in Youngwol prefecture, the TDML was estimated 164-197kg/day and 1,788-2,146kg/day, respectively. This approach will useful for estimating TDML to insufficient watershed of flow data and ungauged watershed of flow data.