Pesticides and deposited fine sediment have independently been associated with changes in relative abundance and species richness in aquatic ecosystems, but the interplay between these two stressors in agricultural streams is poorly understood. A 28-day experiment in outdoor stream mesocosms examined the effects of four levels each of fine sediment coverage (0, 25, 75, 100%) and glyphosate-based herbicide concentration (0, 50, 200, 370 μg/L) on periphyton communities (algae and bacteria) in a fully factorial, repeated-measures design. Our aims were to determine whether (i) increased levels of sediment and glyphosate had individual and/or additive effects, (ii) increased sediment reduced the toxicity of glyphosate (antagonistic multiple stressor interaction), or (iii) sediment-adsorbed glyphosate prolonged the effects of exposure (synergistic interaction). We also assigned all algal taxa to three ecological guilds (low-profile, high-profile and motile growth forms) and separately determined their responses to the treatments. As individual stressors, sediment addition affected all algal community-level metrics, whereas glyphosate addition only affected algal community evenness. Bacterial taxon richness was unaffected by either stressor. In combination, however, significant overall sediment by glyphosate interactions were detected, demonstrating synergistic (algal evenness, high-profile and motile guilds) or antagonistic effects (low-profile guild). Our experiment underscores the importance of considering both structural and functional indicators, including algal guild representation, when assessing the mechanisms by which periphyton communities respond to multiple stressors.