Purpose Assessing the physicochemical characteristics of the stream suspended sediment phase (SSP) is a common component of watershed monitoring, whereas the biological attributes of the SSP are more rarely described. The microbial component is valuable to sediment apportionment studies and can inform on pathogen transport and in-stream biogeochemistry. Methods An established passive, flow-through sampling technique (Phillips Tube (PT) Sampler) was used for time-integrated evaluation of suspended phase microbial communities within an agricultural stream segment (≈ 0.7 km) in southern Ontario, Canada. Monthly DNA-metabarcoding of the SSP was conducted and contrasted with bed sediment phases (BSPs). Results PT samplers showed good spatial precision. Monthly sampled bed sediment microbial communities showed more similarity to each other than to suspended sediment communities. Suspended sediments were characterized by aerobic/facultative aerobic taxa with bed sediments defined by nitrate, iron, and sulfate metabolizing groups. Greater community diversity was observed in BSP samples, with biomarker analysis identifying more unique genera in SSP samples. In situ dissolved oxygen (DO) logging revealed a substantial decrease in PT sampler DO (12 to 3 mg L −1 ) after 3 weeks of deployment. Precipitation events caused in-stream DO concentrations to flatline temporarily, but increased concentrations within samplers. Conclusions PT samplers collected adequate sediment volumes for microbial DNA metabarcoding and showed good replicability. Use of samplers during higher flow periods may collect a more representative microbial community that is less affected by within-sampler decreases in DO. Future use of PT samplers should consider microbial/redox effects that can alter in situ chemistries.