The widespread application of silver in consumer products and the resulting contamination of natural environments with silver raise questions about the toxicity of Ag+ in the ecosystem. Natural organic matter, NOM, which is abundant in water supplies, soil, and sediments, can form stable complexes with Ag+, altering its bioavailability and toxicity. Herein, the extent and kinetics of Ag+ binding to NOM, matrix effects on Ag+ binding to NOM, and the effect of NOM on Ag+ toxicity to Shewanella oneidensis MR-1 (assessed by the BacLight viability assay) were quantitatively studied with fluorous-phase Ag+ ion-selective electrodes (ISEs). Our findings show fast kinetics of Ag+ and NOM binding, weak Ag+ binding for Suwannee River humic acid, fulvic acid, and aquatic NOM, and stronger Ag+ binding for Pony Lake fulvic acid and Pahokee Peat humic acid. We quantified the effects of matrix components and pH on Ag+ binding to NOM, showing that the extent of binding greatly depends on the environmental conditions. The effect of NOM on the toxicity of Ag+ does not correlate with the extent of Ag+ binding to NOM, and other forms of silver, such as Ag+ reduced by NOM, are critical for understanding the effect of NOM on Ag+ toxicity. This work also shows that fluorous-phase Ag+ ISEs are effective tools for studying Ag+ binding to NOM because they can be used in a time-resolved manner to monitor the activity of Ag+ in situ with high selectivity and without the need for extensive sample preparation.