Molybdenum (Mo), tungsten (W), and rhenium (Re) concentrations were measured in the porewaters and sediments of the highly stratified Upper Basin of the Pettaquamscutt River estuary (Rhode Island) to investigate the geochemical processes that influence their concentrations in euxinic systems. Total dissolved sulfide (i.e., ΣS-II) concentrations in the porewaters averaged 3.95 mmol kg−1, whereas the porewaters exhibited average Mo, W, and Re concentrations of 830 nmol kg−1, 69 nmol kg−1, and 7.4 nmol kg−1, respectively. The sediments were subjected to chemical extractions to characterize the reactive fraction (i.e., associated with iron (Fe) monosulfides, Fe/manganese (Mn) oxides/oxyhydroxides, and/or Fe/Mn carbonate minerals) and the pyritized fraction of Mo, W, and Re in the sediments. The reactive fraction of each metal decreased with depth from subsurface maxima near the sediment-water interface, whereas the pyritized fractions exhibited a number of subsurface maxima. Rhenium exhibited the greatest degree of trace metal pyritization (DTMP) in the estuary sediments, followed closely by Mo. Specifically, the DTMP for Re ranged from 75 to 88% and exhibited a mean ( ± 1σ) of 80 ± 4% for the entire sediment core, whereas the DTMP for Mo ranged from 34 to 89% with a mean ( ± 1σ) of 73 ± 18%. In contrast, the DTMP for W was lower, ranging from 48 to 73%, but with a mean ( ± 1σ) of 58 ± 8%. Therefore, about 80%, on average, of the Re and 74% of the Mo that enters the northern portion of the Pettaquamscutt River estuary by the combination of stream water inflow (i.e., Gilbert Stuart Stream) and submarine groundwater discharge (SGD) is eventually fixed within the pyrite fraction of the euxinic bottom sediments. However, only about 60% of the W appears to be fixed in the pyrite fraction in these sediments, whereas the other 40% remains in the reactive sediment pool. We suggest that the different behavior of W compared to Re and Mo in the euxinic porewater and sediments of the Pettaquamscutt River estuary's upper basin reflects, in part, differences in their aqueous speciation and particle reactivity that appears to be dictated by differential uptake and fixation of their respective thioanions (i.e., MoS42−, WS42−, ReS4−) with Fe sulfide minerals.