Sediment traps were deployed inside the anoxic inner basin of Effingham Inlet and at the oxygenated mouth of the inlet from May 1999 to September 2000 in a pilot study to determine the annual depositional cycle and impact of the 1999 La Niña event within a western Canadian inlet facing the open Pacific Ocean. Total mass flux, geochemical parameters (carbon, nitrogen, opal, major and minor element contents, and stable isotope ratios) and diatom assemblages were determined and compared with meteorological and oceanographic data. Deposition was seasonal, with coarser grained terrestrial components and benthic diatoms settling in the autumn and winter, coincident with the rainy season. Marine sedimentary components and abundant pelagic diatoms were coincident with coastal upwelling in the spring and summer. Despite the seasonal differences in deposition, the typical temperate-zone Thalassiosira – Skeletonema – Chaetoceros bloom succession was muted. A July 1999 total mass flux peak and an increase in biogenous components coincided with a rare bottom-water oxygen renewal event in the inlet. Likewise, there were cooler-than-average sea surface temperatures (SSTs) just outside the inlet, and unusually high abundances of a previously undescribed cool-water marine diatom ( Fragilariopsis pacifica sp. nov.) within the inlet. Each of these occurrences likely reflects a response to the strong La Niña that followed the year after the strongest-ever recorded El Niño event of 1997–1998. By the autumn of 1999, SSTs had returned to average, and F. pacifica had all but disappeared from the remaining trap record, indicating that oceanographic conditions had returned to normal. Oxygenation events were not witnessed in the inlet in the years before or after 1999, suggesting that a rare oceanographic and climatic event was captured by this sediment trap time series. The data from this record can therefore be used as a benchmark for identifying anomalous environmental conditions on this coast. ► Only sediment trap study done in a western Canadian inlet facing the open Pacific ► Deposition of settling particles is clearly seasonal. ► Deposition of settling particles is also influenced by the 1999 La Niña event. ► 1999 La Niña had a strong oceanographic and biological effect on the coast. ► Sediment trap data can be used as benchmarks recording anomalous climatic events.