This dataset includes biological, chemical and environmental data associated with marine biogenic silica dynamics collected along the flow path of Pacific-origin waters as they transit through the Arctic. Samples were collected on three cruises: onboard the Canadian Coast Guard Service (CCGS) Sir Wilfrid Laurier (one cruise covering the Bering and Chukchi Seas, Jul 2015), or the CCGS Amundsen (two cruises covering the Canada Basin, Canadian Arctic Archipelago, Baffin Bay and Labrador Sea, Jul-Aug 2015 and Sep 2015). On the CCGS Sir Wilfrid Laurier, seawater sampling was conducted throughout the euphotic zone within (or near) four biological ‘hotspots’ in the northern Bering and Chukchi Seas, as identified by the Distributed Biological Observatory (DBO). On the CCGS Amundsen, seawater sampling was conducted throughout the water column at locations identified as part of the Canadian Arctic GEOTRACES program. Data includes: seawater temperature and salinity, silicic acid, biogenic silica, and lithogenic silica concentrations, and the natural silicon isotopic composition of silicic acid. Data are organized by row, with each row representing a single depth.