Ground water discharge is often a significant factor in the quality of fish spawning and rearing habitat and for highly biologically productive streams. In the present study, water temperatures (stream and hyporheic) and seepage fluxes were used to characterize shallow ground water discharge and recharge within the streambed of Catamaran Brook, a small Atlantic salmon (Salmo salar) stream in central New Brunswick, Canada. Three study sites were instrumented using a total of 10 temperature sensors and 18 seepage meters. Highly variable mean seepage fluxes, ranging from 1.7 × 10−4 to 2.5 cm3 m−2 sec−1, and mean hyporheic water temperatures, ranging from 10.5° to 18.0°C, at depths of 20 to 30 cm in the streambed were dependent on streambed location (left versus right stream bank and site location) and time during the summer sampling season. Temperature data were useful for determining if an area of the streambed was under discharge (positive flux), recharge (negative flux), or parallel flow (no flux) conditions and seepage meters were used to directly measure the quantity of water flux. Hyporheic water temperature measurements and specific conductance measurements of the seepage meter sample water, mean values ranging from 68.8 to 157.9 μS/cm, provided additional data for determining flux sources. Three stream banks were consistently under discharge conditions, while the other three stream banks showed reversal from discharge to recharge conditions over the sampling season. Results indicate that the majority of the water collected in the seepage meters was composed of surface water. The data obtained suggests that even though a positive seepage flux is often interpreted as ground water discharge, this discharging water may be of stream water origin that has recently entered the hyporheic zone. The measurement of seepage flux in conjunction with hyporheic water temperature or other indicators of water origin should be considered when attempting to quantify the magnitude of exchange and the source of hyporheic water.