To investigate the characteristics of ammonium and phosphorus retention in two typical channel forms, deep pool and winding ditch in headwater stream, four field tracer experiments were conducted in a first-order stream of Ershibu River in Hefei suburban, in which a solution of biologically active (NH4Cl and KH2PO4) and conservative (NaCl) tracers was released to the head of each reach at a constant rate. According to the data sets of tracer experiments, mechanisms of ammonium and phosphorus retention were interpreted by using OTIS model code, transient storage metrics and nutrient spiraling theory. Study results showed that: (1) The value of As in deep pool was larger than that in winding ditch, whereas its value of hydrological parameter α was lower by an order of magnitude than that of winding ditch; (2) The value of NH(4)+ -λ in main channel was higher by two to three orders of magnitude than that of NH(4)+ -λs,in transient storage zone in deep pool, but in winding ditch the two parameters were closer in terms of numerical size; (3) In deep pool, the value of NH+(4) -Vf was higher by an order of magnitude than that of SRP-Vf, in winding ditch, however, not only the two values of NH(4)+ -Vf and SRP-Vf were close to each other, but NH(4)+ -Sw was nearly equal to SRP-Sw in numerical size as well; (4) The value of NH(4)+ -U was larger by two to three orders of magnitude than that of SRP-U in deep pool, whereas in winding ditch NH(4)+ -U was just larger by one to two orders of magnitude than SRP-U in size; (5) In general, significant difference existed between deep pool and winding ditch in the effect on ammonium and phosphorus retention, and marked retention efficiency was observed for ammonium rather than SRP in deep pool.