Priority effects are stochastic processes that consider the influence of the order of arrival of species on community dynamics and structure. We evaluated the short-term effects of stream eutrophication and colonization time in freshwater benthic communities (primary producers - periphytic algae, decomposers – fungi, and consumers - macroinvertebrates) to test whether (i) beta diversity is higher in eutrophic streams due to priority effects driven by stochastic community formation processes (ecological drift or random dispersal), and (ii) in the early stages of colonization, priority effects drive the history of the formation and the initial establishment of the community in the stream, resulting in higher beta diversity. The present study was conducted in situ over 28 days in temperate streams along a trophic gradient, with colonization being evaluated every seven days. The study identified 84 species of alga, 43 families of macroinvertebrates, and 44 species of aquatic fungi. Our results demonstrated that deterministic processes were responsible for the formation of aquatic producers, while priority effects (stochasticity) were more important for the aquatic decomposers and consumers. In the case of the producers, beta diversity was highest in the hypertrophic stream, but did not vary significantly over colonization time. The beta diversity of the decomposers was highest in the hypertrophic stream and in the later stages of succession, due primarily to mechanisms of facilitation. The beta diversity of the consumers was lowest in the hypertrophic stream due primarily to the priority and inhibitory effects of the predominant groups, and highest at seven and 21 days of colonization. As these three taxonomic groups differ in their intrinsic biological characteristics, and in their functional role in the ecosystem, our short-term field study demonstrated that both stochastic and deterministic processes combine to influence the configuration of the community, and that the relative importance of the two processes varies systematically along a trophic gradient.