The objective approach for assessment of stream naturalness is an essential part of the stream restoration project. This study proposes the methodology for the assessment of stream naturalness considering physical, biological and chemical factors. Physical factors consists of riffle and pool, river bed material, bank protection, floodplain vegetation and levee materials; biological factors are benthic macroinvertebrate, KSI (Korean Saprobic Index), and IBI (Index of Biological Integrity) and chemical factors are pH, DO (dissolved oxygen), and TP (total phosphorus). This procedure is applied to the Mokgamcheon. As a result, the downstream of Mokgamcheon (zone I) needs the prompt improvement of stream naturalness, compared to the others (zone II and III). This evaluation technique will be an effective tool to quantify the stream naturalness and can be used to set the target of stream restoration project.