Biomonitoring programs to access the ecological integrity of freshwaters tend to rely exclusively on structural parameters. Here we evaluated stream ecological integrity using (a) benthic macroinvertebrate derived metrics and a biotic index as measures of structural integrity and (b) oak litter decomposition and associated fungal sporulation rates as measures of functional integrity. The study was done at four sites (S1, S2, S3 and S4) along a downstream increasing phosphorus and habitat degradation gradient in a small stream. The biotic index, invertebrate metrics, invertebrate and fungal communities' structure and sporulation rates discriminated upstream and downstream sites. Decomposition rates classified sites S4 and S2 as having a compromised ecosystem functioning. Although both functional and structural approaches gave the same results for the most impacted site (S4), they were complementary for moderately impacted sites (S2 and S3), and we therefore support the need for incorporating functional measures in evaluations of stream ecological integrity.