Invasive species are often blamed for the declines of native species, although this is often based on anecdotal or incomplete evidence. In the Virgin River (U.S.A.), the red shiner minnow (Cyprinella lutrensis) has been identified as a major factor in woundfin (Plagopterus argentissimus) decline, a critically endangered endemic minnow. We assessed the evidence for the hypothesis that negative interactions between these two fish drove this decline. We tested three predictions: (1) spatial and temporal patterns were significant predictors of assemblage structure; (2) red shiner would show opposite spatial and temporal patterns to native species; and (3) woundfin would show site-specific decreases in abundance following red shiner invasion. We used a long-term (28 years) dataset of fish abundances in the Virgin River at 10 regularly monitored sites to test our predictions. Using principal coordinates of neighbour matrices with redundancy analysis, we tested our first two predictions by identifying the temporal and spatial structure of the fish assemblages and comparing the patterns of native fish species to those of the invasive fish species. To test our third prediction, we used a breakpoint analysis of site-specific population data to determine if woundfin showed stable populations prior to red shiner invasion, followed by declines after invasion. We found that 42% of variation in fish abundances in the river could be explained by spatial patterns, and 12% by temporal patterns. Red shiner showed opposite spatial and temporal patterns to woundfin (but not to other native species), and abundances of red shiner and woundfin were negatively correlated, yielding correlative evidence of negative interactions between red shiner and woundfin. However, our breakpoint analysis did not show the expected patterns and woundfin declined even in sites that did not experience red shiner invasion pointing to alternate mechanisms of decline such as effects of poor water quality. Our analyses provided correlative but conflicting evidence of red shiner influence on woundfin but were unable to identify a definitive causal mechanism of woundfin decline. We discuss two possible explanations for the contemporary woundfin decline and red shiner invasion: displacement of woundfin via negative interactions, or replacement of woundfin by red shiner in a niche already vacated by woundfin due to environmental or anthropogenic disturbances. This study demonstrates that the dynamics between native and non-native species may not be straightforward and can be complicated by other factors such as anthropogenic activities and environmental changes. This research highlights that long-term monitoring is essential to untangling interactions between native and invasive species to develop effective conservation methods that address underlying causes of decline.