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The influence of hydraulic exchange patterns on hyporheic water chemistry and invertebrate community composition was measured in three gravel-bed rivers of southern Hawke’s Bay, North Island, New Zealand. Based on patterns reported overseas we predict that down-welling waters will be similar to surface waters in chemical characteristics and epigean animals will be more common in down-welling waters than in up-wellings, which would have a different chemical signature to the surface waters and a fauna dominated by hypogean invertebrates. Conductivity, pH, and temperature of hyporheic water were least like those of surface waters at up-wellings in the groundwater-fed Makaretu River. Only 6% of the invertebrate fauna of these up-wellings comprised epigean animals. In contrast, in the groundwater-recharging Tukituki and Waipawa Rivers, hyporheic water chemistry was similar to that of surface water in down-wellings and 40% of the community comprised epigean animals by abundance. Significant increases (P < 0.05) in species diversity and taxonomic richness was also identified in down-welling zones compared with up-wellings. Species diversity and taxonomic richness were lowest in up-wellings in the Makaretu where hypogean animals dominated the hyporheic fauna. Species diversity and taxonomic richness were higher in down-wellings than up-wellings because more epigean taxa were present.