Body size is perhaps the most fundamental property of an organism and its relationship with abundance is one of the most studied relationships in ecology. Although numerous studies have examined these relationships in local communities, few have investigated how they vary at different temporal and spatial scales. We investigated the relationship between body size and abundance of local macroinvertebrate communities in two floodplain channels of the French upper Rhone River. The two channels differ in their vegetation coverage (high vs. low vegetation) and hydrological regimes. The shapes of the size-abundance relationship were similar between channels on a yearly basis but differed when compared between months. The variation in local size-abundance relationships between months was related to variation in the functional diversity across time. Our findings suggest that local size-abundance relationships are able to quantitatively describe temporal changes in community structure, showing the importance of relating diversity with ecosystem function in a more realistic context.