Trace element concentrations in marine pyrite, measured by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS), have the potential to open a new window into deep-time ocean chemistry, atmosphere oxygenation, and genesis of basin-hosted ore deposits. Only early-formed syngenetic and early diagenetic marine pyrite preserves the trace element chemistry of the past oceans, as late diagenetic and metamorphic recrystallization of pyrite changes the trace element budget. A database of over 5,000 marine pyrite trace element analyses by LA-ICP-MS has enabled the development of deep-time proxies for nutrient supply, productivity, ocean pH, and atmosphere oxygenation. These proxies suggest that the Archean ocean was enriched in Fe, Ni, Co, As, Au, and Hg compared with modern oceans, probably related to composition of erosive flux from the continents and active seafloor hydrothermal activity. This was also a time for major iron, gold, and nickel ore formation in sedimentary and greenstone settings. In the Paleoproterozoic, there was a decrease in Ni, Co, As, and Au, replaced by increasing Cu, Zn, and in the oceans and O2 in the atmosphere. The first appearance of red beds and evaporites is a response to the rise in O2 and , and provided the conditions necessary for sediment-hosted Cu and stratiform Pb-Zn-Ag sedimentary exhalative (SEDEX) deposits. Through 1700 to 1500 Ma, phosphorous, gold, and most other nutrient trace elements dropped to a minimum in the ocean, possibly related to tectonic stasis and changes in atmosphere O2 and/or ocean pH. Sediment-hosted Au, orogenic Au, and volcanic-hosted massive sulfide (VHMS) deposits are virtually absent from this period, whereas mineral systems that required relatively oxidized ore fluids, such as SEDEX Zn-Pb, iron oxide copper-gold (IOCG), and unconformity uranium became more abundant, due to these changed conditions. All redox-sensitive and nutrient trace elements rose dramatically in concentration at the Proterozoic-Phanerozoic boundary and peaked in the mid- to Late Cambrian oceans, accompanied by black shale deposition enriched in Mo, Se, Ni, Ag ± Au, and platinum group elements. Cyclic variation in nutrient trace elements increased in frequency through the Phanerozoic on a wavelength of 50 to 100 m.y., compared with 500 to 1,000 m.y. in the Proterozoic. The more frequent Phanerozoic cycles relate to repeated episodes of continent collision, mountain building, and increased erosive flux of trace elements into the oceans. Ore deposit cycles in the Phanerozoic of SEDEX Zn-Pb, orogenic sediment-hosted Au, and VHMS have a time frame similar to the tectonic and seawater chemistry cycles.