The biogeochemistry of iron sulfide minerals in the water column of the Cariaco Basin was investigated in November 2007 (non-upwelling season) and May 2008 (upwelling season) as part of the on-going CARIACO (CArbon Retention In A Colored Ocean) time series project. The concentrations of particulate sulfur species, specifically acid volatile sulfur (AVS), greigite, pyrite, and particulate elemental sulfur, were determined at high resolution near the O2/H2S interface. In November 2007, AVS was low throughout the water column, with the highest concentration at the depth where sulfide was first detected (260 m) and with a second peak at 500 m. Greigite, pyrite, and particulate elemental sulfur showed distinct concentration maxima near the interface. In May 2008, AVS was not detected in the water column. Maxima for greigite, pyrite, and particulate elemental sulfur were again observed near the interface. We also studied the iron sulfide flux using sediment trap materials collected at the Cariaco station. Pyrite comprised 0.2–0.4% of the total particulate flux in the anoxic water column, with a flux of 0.5–1.6 mg S m−2 d−1.