Understanding the role of different rainfall scenarios on faecal indicator organism (FIO) dynamics under variable field conditions is important to strengthen the evidence base on which regulators and land managers can base informed decisions regarding diffuse microbial pollution risks. We sought to investigate the impact of low intensity summer rainfall on Escherichia coli-discharge (Q) patterns at the headwater catchment scale in order to provide new empirical data on FIO concentrations observed during baseflow conditions. In addition, we evaluated the potential impact of using automatic samplers to collect and store freshwater samples for subsequent microbial analysis during summer storm sampling campaigns. The temporal variation of E. coli concentrations with Q was captured during six events throughout a relatively dry summer in central Scotland. The relationship between E. coli concentration and Q was complex with no discernible patterns of cell emergence with Q that were repeated across all events. On several occasions, an order of magnitude increase in E. coli concentrations occurred even with slight increases in Q, but responses were not consistent and highlighted the challenges of attempting to characterise temporal responses of E. coli concentrations relative to Q during low intensity rainfall. Cross-comparison of E. coli concentrations determined in water samples using simultaneous manual grab and automated sample collection was undertaken with no difference in concentrations observed between methods. However, the duration of sample storage within the autosampler unit was found to be more problematic in terms of impacting on the representativeness of microbial water quality, with unrefrigerated autosamplers exhibiting significantly different concentrations of E. coli relative to initial samples after 12-h storage. The findings from this study provide important empirical contributions to the growing evidence base in the field of catchment microbial dynamics.