Complex marine-terrestrial interactions characterize Chilean fjords, where benthic communities influence the distribution of organic matter (OM). We examined spatial and seasonal changes in the hydrography, sediment conditions and soft-bottom macrobenthic, meiobenthic, and total microbial biomass in a glacial Patagonian fjord (Martinez Channel, Chile). The transport of a high load of glacial mineral and particulate OM to the fjord in the austral summer coincided with low total live benthic biomass. Multivariate analysis evidenced temporal-related macrofaunal groups influenced by the different environments produced by the advection of sediment transport and terrestrial OM from the Baker River, Chile. The relationships between density/biomass and respiration versus body size varied considerably with distance from major riverine inputs, but the slopes of density size spectra and normalized biomass size spectra were less negative in summer than in winter. Occasional large-scale advective processes in the water column affected sediment conditions and removed surface macrofauna, influencing the slope and intercept of the regression models. In the outer fjord, lateral advection and subsequent sedimentation of terrestrial OM contributed a significant fraction to total OM sediments (<14.76%). Stable carbon isotopes measured in benthic organisms suggest that benthic communities in the inner fjord may assimilate a significant fraction of terrestrial OM via heterotrophic bacteria in contrast to the minor input of terrestrial OM in the outer fjord.