Human modification of freshwater ecosystems can impact biodiversity by impeding gene-flow between fragmented populations. This might be in the form of direct physical barriers (e.g., dams) or indirect deterrents to traversal (e.g., pollution). The negative consequences of dams on population connectivity are well-documented, but indirect impacts are often difficult to quantify. We used a population genetics approach across three river catchments in Hong Kong to show that gene flow is lower between fish populations that are bisected by artificial stream channels, even in the absence of physical barriers. This was mediated by riparian vegetation—channelisation decreases the density of riparian vegetation, which in turn deters fish passage to reduce gene flow across channelised river segments. Fish susceptibility to indirect channelisation impacts varied with species traits, and habitat specialists that are also poor swimmers appear to be particularly vulnerable. Stream rehabilitation seeks to reverse the impacts of channelisation by reintroducing natural elements (e.g., vegetation, natural stream beds). We found that this was effective in mitigating the impacts of channelisation, and gene flow was broadly comparable across unmodified and rehabilitated stream segments.