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Conservation planning and biodiversity monitoring rely exclusively on the use of surrogate groups. However, the effectiveness of these groups in representing unknown biodiversity is rarely tested. These tests can be based on cross-taxon concordance (or congruence) analysis. In a second step, the main mechanisms underlying concordance can be investigated. Here, we evaluated the relative influence of local environmental factors and spatial processes on the patterns of beta-diversity exhibited by phytoplankton, zooplankton and benthic invertebrates and the strength of assemblage concordance among these assemblages in 38 upland Amazonian lakes (northern Brazil) over four years. Zooplankton and benthic invertebrates responded exclusively to environmental variables. These results are in accordance with the expected under the species sorting model, where local factors are the main mechanisms shaping assemblage structure. In general, patterns of concordance between the assemblages were weak and varied through time, indicating that the use of surrogates in freshwater ecosystems may be a flawed approach.