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1. Hydrological exchange between the surface stream and the hyporheic zone is well documented in the main channel of rivers, especially at the reach scale. Hydrological processes of advection/convection occur at different scales, and in secondary channels of large rivers little is known about these exchanges in the hyporheic zone on a broad scale (i.e. kilometres). This work studied exchanges of water and biota in a secondary channel on a large scale (4 km), using a three-dimensional framework.

2. The exchanges of water were described using physicochemical indicators of surface and groundwaters. Samples of water and biota were taken in three dimensions: (i) vertically from benthic (i.e. 0.20 m below the surface of the substratum) to hyporheic (0.50 m) and deep interstitial (1.0 m) zones; (ii) laterally from the right to the left bank (i.e. right, middle and left positions); and (iii) longitudinally from upstream to downstream (seven stations regularly distributed along the channel).

3. The physicochemical indicators clearly revealed hydrological heterogeneity in the longitudinal and vertical dimensions, whereas lateral variability was not significant.

4. Spatial distribution of biota exhibited strong longitudinal variations that were not gradual as predicted by an upstream/downstream continuum, but patchy and discontinuous. No significant differences were found between the three positions across the channel.

5. Analyses of both physicochemical and faunal data sets produced matched ordination of samples and stations, indicating that interstitial–surface flow relationships appear to be an important governing factor in the distribution of interstitial biota at this broad scale.

6. Results are discussed in relation to the hypothetical three-dimensional models of the hyporheic zone in rivers. Contrasting with other observations on the main channel (where advection/convection patterns are dominated by morphological changes of the river-bed morphology), it is proposed that water exchanges in backwaters are more likely to be related to local modifications of stream-bed porosity.