The datasets were acquired to estimate whole stream metabolism (photosynthesis, respiration).Photosynthetic active radiation, atmospheric pressure, stream water discharge, water temperature and dissolved oxygen concentrations were recorded at five-minute time intervals at six stations (three stream reaches) along two parallel first order streams: Cairn Burn (May 2007-July 2008) and Birnie Burn (May 2007-October 2007).In addition, stream reach parameters necessary to calculate mean travel time, oxygen reaeration coefficient and proportion of base flow under varying discharge are given with their uncertainties. The forms of the equations to calculate mean travel time τ [min], oxygen reaeration coefficient k2 [/min] and proportion of base flow p(Q_b) [range 0 to 1] are:τ=aQ^bk2=aQ+bp(Q_b)=1/(1+exp(a*ln(Q)-b))with discharge Q [l/s] taken as Q_ECN for Birnie Burn and Q_C1 for Cairn Burn.The discharge for stations upstream of the calibrated flumes were also calculated after corrections for lateral inflows determined by tracer studies. The streams undercut the banks so two stream widths were given: wetted stream bed width (recommended to use in stream metabolism calculations) and open width (recommended to calculate amount of light available to stream bed). Stream reach length is also given.