Recreational water quality of rivers is typically assessed by microbial analysis of indicator organisms, such as Escherichia coli and enterococci in samples collected directly from the water column, implying that risk to public health comes from free-floating microorganisms. In New Zealand, the Recreational Water Quality Guidelines apply certain E. coli concentration thresholds to categorize results into ‘meet guidelines’ (≤ 260 cfu E. coli 100 mL−1), ‘alert level’, and ‘action level’ (≥ 550 cfu E. coli 100 mL−1). The impairment of water quality due to re-suspended riverbed sediment under flood conditions has been widely recognized. However, the potential risks posed by sediment-linked microorganisms associated with river recreational activities under base flow are less appreciated. We evaluated the water quality of 30 rivers in Canterbury, New Zealand, during base flow conditions prior to and after artificially stirring the sediment. Bacterial and protozoan indicators, pathogens, water quality, and land use in surrounding areas were examined. While 71% of water samples (n = 64) met New Zealand Recreational Water guidelines prior to stirring, only 39% of samples (n = 35) met the guidelines after stirring. E. coli levels increased by 110%, or more, following sediment stirring. Campylobacter were detected in every river, at least once, and increases were observed following stirring. We conclude that sediment-associated microbes become suspended by recreational activities and may pose a higher risk than previously thought to river users. To ensure public health is protected, authorities should assess microorganisms in both sediment and water samples to rate the microbiological risk of recreational water use.