There are many field techniques used to quantify rates of hyporheic exchange, which can vary in magnitude and direction spatially over distances of only a few metres, both within and between morphological features. We used in-stream mini-piezometers and heat transport modelling of stream and streambed temperatures to quantify the rates and directions of water flux across the streambed interface upstream and downstream of three types of in-stream geomorphic features: a permanent dam, a beaver dam remnant and a stream meander. We derived hyporheic flux estimates at three different depths at six different sites for a month and then paired those flux rates with measurements of gradient to derive hydraulic conductivity (K) of the streambed sediments. Heat transport modelling provided consistent daily flux estimates that were in agreement directionally with hydraulic gradient measurements and also identified vertical heterogeneities in hydraulic conductivity that led to variable hyporheic exchange. Streambed K varied over an order of magnitude (1·9 × 10−6 to 5·7 × 10−5 m/s). Average rates of hyporheic flux ranged from static (q < ±0·02 m/day) to 0·42 m/day. Heat transport modelling results suggest three kinds of flow around the dams and the meander. Copyright © 2010 John Wiley & Sons, Ltd.