Because of water transfers through fissures, cavities, caves and phreatic channels of various sizes and unknown directions, the topographic watersheds of karst catchments have little significance for their aquifers. Most of the flow in the Manavgat River in South Anatolia has its origin outside of the surface watershed and is transferred through karst pathways. Previous investigations found evidence for this by groundwater tracing techniques. In this study, flow recession analysis and baseflow separation are applied to the time series of daily flows 1992-2008 from three gauging stations. Flow recessions were found corresponding to the nonlinear storage-baseflow relationship S=. a·. Q^b, with b values around 0.5 as typical for unconfined groundwater, while the coefficient a showed marked seasonal variations with higher values in the rainy winter time and decreasing values towards the dry summer. For catchments which receive water transfers from other areas, the decrease of a is retarded. Flow recession is slower since more water is available. Baseflow separation by using the same nonlinear model revealed that direct flow, which is mainly surface flow, corresponds roughly to the surface catchments while baseflow, which accounts for most of the total flow, is highly influenced by transfers from karst sink areas outside the surface watersheds. The subsurface transfer was simulated by a nonlinear reservoir routing algorithm. Time series of monthly baseflow from catchments which receive transfer water were compared with those of sinkhole (loss) areas. The procedure allows inferring the origin area of the inflows and estimating the retention or lag time of the transfer.