Spatial synchrony occurs when the abundance of populations in different locations rise and fall together. This pattern is caused mainly by dispersal and spatially correlated environmental stochasticity. The levels of spatial synchrony can vary between species, yet little is known about which species traits can explain this interspecific variation. In addition, traits may have different degrees of influence on spatial synchrony levels because of their differences in plasticity. We hypothesized that conservative traits—reproductive and morphological—will best explain interspecific variation in synchrony, while those that may vary according to the environment—feeding and habitat preference—will be weakly related to this interspecific variation. We evaluated the spatial synchrony of freshwater fish species in a highly fragmented river in the Neotropical region and related the levels of synchrony to seven predictors: diet, reproductive traits (migration, fecundation, parental care and spawning), position in the water column, niche breadth, body size, body shape and average temporal occurrence of each species. The fish species showed low levels of spatial synchrony but a high interspecific variation (correlation values ranging from −0.11 to 0.41). We found that this variation was mainly related to species' reproductive traits, that is, sedentary species with partial spawning and without parental care had higher mean spatial synchrony than species with the opposite characteristics. In contrast, more plastic traits (diet and habitat preferences) were poor predictors of mean spatial synchrony. We speculate that, despite the low spatial synchrony found, if extreme impacts continue to occur in the basin at the regional scale, it may negatively affect local fish populations in a synchronous manner, resulting in increased risk of simultaneous declines.