Filtration products containing silver nanoparticles (Ag-NPs) have been used for water purification to provide drinking water for humans. However, it is unclear if differences in water chemistry influence their effectiveness or whether the presence of Ag in the filtrate (drinking water) impacts the gut microbiome. Using water samples differing markedly in chemical properties, we have found that ≥99.89% of E. coli were killed in all cases, regardless of the water chemistry. However, in the first 25 mL of filtration, concentrations of Ag in most of the water samples (0.14–45.2 mg L−1) exceeded the limit for drinking water (0.1 mg L−1), differing depending upon water chemistry. Synchrotron-based X-ray absorption spectroscopy analysis revealed that up to 36% of the Ag in the filter paper was present as AgNO3 and 64% as Ag-NPs, with this AgNO3 likely contributing to the high Ag concentrations in the filtrate. Finally, we also examined the impacts of oral gavage of the Ag-containing filtrate on the mouse gut microbiome. It was found that Ag from the filtrate accumulated mainly in the liver and kidneys. In female mice, we also found that the Ag-containing filtrate increased the relative abundance of Bacteroidetes in the faeces, whilst decreasing that of Firmicutes. Our data indicate that although Ag-NP-containing filter products have excellent antimicrobial properties, the high concentrations of Ag in the filtrate are potentially of concern for the gut microbiome and further work is required in this regard.