The anelastic structure of a subduction zone can place first‐order constraints on variations in temperature and volatile content. We investigate seismic attenuation across the western Pacific Mariana subduction system using data from the 2003–2004 Mariana Subduction Factory Imaging Experiment. This 11‐month experiment consisted of 20 broadband stations deployed on the arc islands and 58 semibroadband ocean bottom seismographs deployed across the fore arc, island arc, and back‐arc spreading center. We compute amplitude spectra for P and S arrivals from local earthquakes and invert for the path‐averaged attenuation for each waveform along with the seismic moment and corner frequency for each earthquake. Additionally, we investigate earthquake source parameter assumptions and frequency‐dependent exponents (α) ranging from 0 to 0.6. Tomographic inversion of nearly 3000 t* estimates (at α = 0.27) for 2‐D Q _P ⁻¹ and Q _P /Q _S structure shows a ∼75 km wide columnar‐shaped high‐attenuation anomaly with Q _P ∼ 43–60 beneath the spreading center that extends from the uppermost mantle to ∼100 km depth. A weaker high‐attenuation region (Q _P ∼ 56–70) occurs at depths of 50–100 km beneath the volcanic arc, and the high‐attenuation regions are connected at depths of 75–125 km. The subducting Pacific plate is characterized by low attenuation at depths greater than 100 km, but high attenuation is found in the plate between 50 and 100 km depth. The fore arc shows high attenuation near the volcanic arc and beneath the serpentinite seamounts in the outer fore arc. Q _S structure is less well resolved than Q _P because of a smaller data set, but Q _P /Q _S ratios are significantly less than 2 throughout the study region. As temperatures estimated from Q _S ⁻¹ are unusually high, we interpret the arc and wedge core anomalies as regions of high temperature with enhanced Q ⁻¹ due to hydration and/or melt, the slab and fore‐arc anomalies as indicative of slab‐derived fluids and/or large‐scale serpentinization, and the columnar‐shaped high Q _P ⁻¹ anomaly directly beneath the back‐arc spreading center as indicative of a narrow region of dynamic upwelling and melt production beneath the slow spreading ridge axis.