Sedimentary pyrite formed in the water column, or during diagenesis in organic muds, provides an accessible proxy for seawater chemistry in the marine rock record. Except for Mo, U, Ni and Cr, surprisingly little is known about trace element trends in the deep time oceans, even though they are critical to developing better models for the evolution of the Earthʼs atmosphere and evolutionary pathways of life. Here we introduce a novel approach to simultaneously quantify a suite of trace elements in sedimentary pyrite from marine black shales. These trace element concentrations, at least in a first-order sense, track the primary elemental abundances in coeval seawater. In general, the trace element patterns show significant variation of several orders of magnitude in the Archaean and Phanerozoic, but less variation on longer wavelengths in the Proterozoic. Certain trace elements (e.g., Ni, Co, As, Cr) have generally decreased in the oceans through the Precambrian, other elements (e.g., Mo, Zn, Mn) have generally increased, and a further group initially increased and then decreased (e.g., Se and U). These changes appear to be controlled by many factors, in particular: 1) oxygenation cycles of the Earthʼs ocean–atmosphere system, 2) the composition of exposed crustal rocks, 3) long term rates of continental erosion, and 4) cycles of ocean anoxia. We show that Ni and Co content of seawater is affected by global Large Igneous Province events, whereas redox sensitive trace elements such as Se and Mo are affected by atmosphere oxygenation. Positive jumps in Mo and Se concentrations prior to the Great Oxidation Event (GOE1, c. 2500 Ma) suggest pulses of oxygenation may have occurred as early as 2950 Ma. A flat to declining pattern of many biologically important nutrient elements through the mid to late Proterozoic may relate to declining atmosphere O2, and supports previous models of nutrient deficiency inhibiting marine evolution during this period. These trace elements (Mo, Se, U, Cu and Ni) reach a minimum in the mid Cryogenian and rise abruptly toward the end of the Cryogenian marking the position of a second Great Oxidation Event (GOE2).