AbstractDespite important advances in the ecology of river food webs, the strength and nature of the connection between the meio‐ and macrofaunal components of the web are still debated. Some unresolved issues are the effects of the inclusion of meiofaunal links and their temporal variations on the overall river food web properties, and the significance of autochthonous and allochthonous material for these components. In the present study, we conducted analyses of gut content of macro‐ and meiofauna and stable isotope analyses of meiofauna to examine seasonal food webs of a chalk stream. The results of the gut content analyses, confirmed by the δ13C signatures, revealed a seasonal shift from a dependence on autochthonous (biofilm) to allochthonous food sources. Here, we demonstrate that aggregating basal or meiofaunal species into single categories affects key web properties such as web size, links, linkage density, and predator–prey ratios. More importantly, seasonal variation in attributes characterized the entire web and these changes persist regardless of taxonomic resolution. Furthermore, our analyses evidenced discrete variations in δ15N across the meiofauna community with a trophic structure that confirms gut content analyses, placing the meiofauna high in the food web. We, therefore, conclude that small‐body‐sized taxa can occur high in dynamic river food webs, questioning assumptions that trophic position increases with body size and that webs are static.