Concentrations of the fecal indicator bacteria (FIB) Escherichia coli and enterococci are used to assess microbial impairment in irrigation and recreation water sources. Whereas the FIB concentrations’ variability at large temporal scales such as seasons, and large spatial scales encompassing different land use has been studied, the knowledge about smaller‐scale variability remains sparse. This work aimed to research the small‐scale variability of E. coli and enterococci in a montane creek with sandy bottom sediments. Sediment samples were collected weekly for a year in triplicate at sampling sites in a forested headwater, an agricultural area, and a mixed urban‐agricultural area. The average weekly change in concentrations was from two times at the forested site to five times at the urban‐agricultural site. Mean relative deviations from averages across sampling locations increased from ‐25% at the forested site to 45% at the urban‐agricultural site. This trend was also observed separately over cold and warm seasons. Over a week without precipitation, E. coli concentrations decreased on average by 20% in warm period and by45% in cold period; the enterococci concentration declined by 12% in both cold and warm periods. The sediment particle size distributions were significantly different among the three sites and between cold and warm seasons. Rankings of sediment fine mass fractions and FIB concentrations were positively correlated at two of three sampling sites in more than 70% of observation dates. The results of this work indicate the need to evaluate the uncertainty of sediment FIB concentrations before designing sediment FIB monitoring quality.This article is protected by copyright. All rights reserved