From 2009 to the present, diatom periphyton communities have been collected as part of a long-term monitoring program summer and fall between Sunbury and Selinsgrove on a transect near Shady Nook, Byers Island on the Susquehanna River. The overall purpose of the monitoring program was to establish a baseline together with benthic invertebrate communities to help understand changes in the Susquehanna River. Throughout the study, diatom communities were collected passively by periphytometers, artificial substrates using glass microscope slides which were immersed in the river for 3-4 week intervals. In 2012, we began to supplement the passive samples with diatom communities collected actively from stones, sediment, and plants (when present). Overall, species richness for the sites was relatively low and rarely exceeded 15 species when collections were made by periphytometers, but more than doubled (26-56) when collections were made by active means. Furthermore, from 2012 to the present Cocconeis placentula dominated the passive collections (x" = 81.7%), but were much less common in diatom communities on stone (x" = 7.8%) and sediment (x" = 6.0%). This difference was seen in common metrics like Shannon Diversity Index (SDI) in which SDI for diatom communities on glass slides was 0.5 to 0.8 while SDI values for communities on stone and sediment ranged from 2.5 to 3.0. The Byers Island transect lies below the confluence of the West Branch and North Branch of the Susquehanna River, each of which shows signature values of turbidity, pH, conductivity, and alkalinity. Because of the dominance of C. placentula on the periphytometer slides, diatom communities on them showed high similarity between the two plumes. Communities collected by active means, however, did show differences. For example, of the 146 species collected between samples taken actively in 2013 from the North Branch Plume and West Branch Plume, only 20 species were shared between them. That the level of homogeneity between samples may be a consequence of the homogeneity or orientation of the substrates will be discussed.