In Clear Creek, which runs through the Iowa State University campus in Ames, Iowa, USA, several types of iron mineralisation occur within stagnant pools and slow-moving water. This includes rusty flocs, commonly observed in mineral springs, rust-stained sediments and iridescent films (‘schwimmeisen’) on the pool surfaces. Observations of iron mineralisation over the course of more than a year in a single reach indicated that mineralisation occurred after precipitation events once water levels in the stream had dropped. Iron extracted and quantified from Clear Creek sediments and pool waters indicated the stream and its sediments were unlikely to be supplying the iron for mineralisation. We hypothesise that the observed mineralisation could result from the discharge of shallow, reducing groundwater-bearing Fe(II) into stagnant pools that form in debris-dammed areas of the stream. Piezometers installed next to the creek documented that shallow groundwater contained dissolved Fe, with the source of Fe being the floodplain sediments and the hydraulic gradient promoted groundwater discharge into the stream. Microorganisms identified in mineralised pools using 16S rRNA amplicon sequencing revealed an elevated presence of putative iron-oxidizing and iron-reducing microorganisms in mineralised vs. non-mineralised pools. Further investigation of the iridescent films revealed them to be composed of amorphous Fe(III) minerals. We further hypothesise that microbial exudates reduce surface tension and potential micro-zones for subsequent microbial iron redox cycling with dissolved organic matter in the pools. Determining the processes controlling mineralisation can lead to a better understanding of the ecological role of iron mineralisation in agricultural watersheds and the importance of contaminant degradation and nutrient cycling.