Pharmaceutical residues in sediments are concerning as ubiquitous emerging contaminants. Pyrite is the most abundant sulfide minerals in the estuarine and coastal sediments, making it a major sink for pharmaceutical pollutants such as sulfamethoxazole (SMX). However, research on the adsorption and redox behaviors of SMX on the pyrite surface is limited. Here, we investigated the impact of the nonphotochemical process of pyrite on the fate of coexisting SMX. Remarkably, sulfur vacancies (SVs) on pyrite promoted the generation of nonradical species (hydrogen peroxide, H2O2 and singlet oxygen, 1O2), thereby exhibiting prominent SMX degradation performance under darkness. Nonradical 1O2 contributed approximately 73.1% of the total SMX degradation. The SVs with high surrounding electron density showed an advanced affinity for adsorbing O2 and then initiated redox reactions in the sediment electron-storing geobattery pyrite, resulting in the extensive generation of H2O2 through a two-electron oxygen reduction pathway. Surface Fe(III) (hydro)oxides on pyrite facilitated the decomposition of H2O2 to 1O2 generation. Distinct nonradical products were observed in all investigated estuarine and coastal samples with the concentrations of H2O2 ranging from 1.96 to 2.94 μM, while the concentrations of 1O2 ranged from 4.63 × 10-15 to 8.93 × 10-15 M. This dark-redox pathway outperformed traditional photochemical routes for pollutant degradation, broadening the possibilities for nonradical species use in estuarine and coastal sediments. Our study highlighted the SV-triggered process as a ubiquitous yet previously overlooked source of nonradical species, which offered fresh insights into geochemical processes and the dynamics of pollutants in regions of frequent redox oscillations and sulfur-rich sediments.