Microbial communities play integral roles in biogeochemical cycles through coupled metabolic processes that give rise to higher order ecosystem functions and services. Their importance is especially acute in productive coastal ecosystems, like the coastal temperate rainforest of British Columbia (BC), where large amounts of organic matter (OM) can be rapidly exported from land to sea. In 2013, the Hakai Institute established a long-term research program on Calvert Island, BC that seeks to understand the seaward flux of terrestrial materials in a region where very little is known about the contribution of terrestrial OM to coastal ocean food webs. As part of this program, we sampled the soils and major streams of Calvert Island and the adjacent marine system, Kwakshua Channel, throughout 2013-2015 to compare microbial community structure and function across the coastal temperate rainforest landscape and into the sea. Here, we highlight the first year of community sequencing data to show the distinctness of microbial communities across this land-sea continuum and the flux of terrestrial microbes into coastal waters during storm events. Seasonal variability in marine community composition appears to be driven by physical processes, such as upwelling, and OM source, especially in surface waters, where the balance between terrestrial- and phytoplankton-derived OM is constantly in flux. Observations of soil and stream microbial taxa in the marine system highlight the connectivity, even at the microbial level, between land and sea in coastal margin ecosystems.