Given the well-known risks of hexavalent chromium (Cr(VI)) to both human health and the environment, it is of utmost importance to develop robust and effective techniques for the removal of this hazardous compound during wastewater treatment. To this end, we present a facile method to synthesize an efficient heterogeneous catalyst that can be used in continuous flow catalysis for the reduction of Cr(VI) to trivalent chromium (Cr(III)) in water. A seed-mediated growth strategy of island growth mode was adopted to synthesize Pd–AuAg trimetal nanohybrids with different heterogeneous structures: octapod-like, bumpy, and Janus structures. When evaluated in batch-type catalysis, the as-synthesized Pd–AuAg trimetal nanohybrids showed excellent catalytic activity toward the reduction of Cr(VI) in water. Continuous flow catalysis was carried out by synthesizing a nanocomposite hydrogel with the Pd–AuAg trimetal nanohybrids embedded and using it as a heterogeneous catalyst. The experimental results showed that the catalytic activity of the nanocomposite hydrogel in the flow reaction could be effectively controlled by adjusting the composition of the hydrogel constituents and the processing conditions such as the flow rate. Outstanding catalytic activity, as indicated by a conversion rate of 98%, was achieved under optimized conditions. In addition, the nanocomposite-based heterogeneous catalyst exhibited excellent stability and could be reused without substantial loss of activity even when stored for an extended period in the dried state.