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Habitat degradation is one of the major reasons for freshwater species decline. Hydrogeomorphological processes (such as sediment transport, bank erosion, and flooding) operate at the catchment scale and determine habitat features in river reaches. However, habitat quality indices and restoration for freshwater fish species are often implemented at small spatial scales of a few hundred metres. The Morphological Quality Index (MQI) considers fluvial processes at larger scales as well as channel forms, human impacts, and historical changes, but few studies have assessed its relevance for ecosystem health. We investigated relationships between the MQI, habitat quality (using the Qualitative Habitat Evaluation Index, QHEI), land cover, and fish metrics (number of fish species, index of biotic integrity (IBI), and trout biomass) in 26 salmonid streams in Aotearoa New Zealand and Southern Ontario, Canada. We found a significant correlation between the MQI and QHEI, and both metrics were correlated with urban and native forest proportion in the catchment. However, we found no relation between the MQI and the proportion of agricultural land in the catchment, while the QHEI was correlated with agricultural land in the riparian zone, highlighting the importance of vegetated riparian buffers in providing fish habitat. Establishing a strong correlation with fish metrics remains challenging. Nevertheless, a modified MQI targeting ecological health could be used as an effective management tool for aquatic conservation.