High dissolved iron (dFe) concentrations of the order of 10–100 nmol L−1 are a feature of waters influenced by sedimentary inputs in oxygen minimum zones (OMZ). However, the temporal development of dFe concentrations is poorly defined due to a general reliance on snapshot cross-shelf sections to study marine trace metal dynamics. Multiple cruise campaigns since the 1980s have investigated Fe dynamics over the Peruvian shelf, particularly between 9° S and 17°S where the shelf is broad, extremely productive and known to feature benthic dFe effluxes which are amongst the highest measured globally. This extensive long-term dataset uniquely allows us to study the interannual variability in dFe concentrations and their response to El Niño–Southern Oscillation (ENSO) events. By combining data from 11 cruises during the period 1984–2017 we are able to evaluate dFe dynamics on interannual timescales in a major OMZ. The region where average dFe concentrations are sensitive to variations in ENSO is confined to a subsurface layer at depths between 50 and 150 m, particularly in the narrow coastal region within 50 km of the coastline. Subsurface dFe concentrations were generally low during El Niño events (0.7–15.4 nmol L−1) and relatively high with a wider range of variability during the cold ENSO phase (1.1–52.1 nmol L−1). Inverse relationships between wind speed and surface/subsurface dFe were evident. In the subsurface layer, this may be attributable to enhanced dFe offshore transport along isopycnals when upwelling-favorable winds relax in accordance with previously outlined theories. Surface layer (<40 m) dFe variability was likely associated with a dilution and/or oxidation effect depending on the strength of wind driven water column mixing. Upwelling brings macronutrient-rich water into the euphotic zone, but its intensity had a limited impact on upper layer dFe concentrations possibly due to the influence of an onshore geostrophic flow. Interannual variability in surface chlorophyll-a (Chl-a) was found to correlate with dFe concentration in the offshore zone of northern Peru. This is consistent with bioassay experiments and climatological residual nitrate concentrations which both indicate proximal Fe limitation of phytoplankton growth over and beyond the northern Peruvian shelf. Overall, our work highlights the importance of physical factors driving short-term variations in Fe availability in one of the world’s most economically important fishery regions and suggests that, despite pronounced spatial and temporal variability in dFe concentrations, the ENSO phase has an impact on dFe availability.