Environmental DNA (eDNA) metabarcoding can rapidly characterize the composition and diversity of benthic communities. As such, it has high potential utility for routine environmental assessments of benthic impacts of marine finfish farming. In this study, 126 sediment grab samples from 42 stations were collected along an organic enrichment gradient at six salmon farms in British Columbia, Canada, and benthic biotic community changes were assessed by both eDNA metabarcoding of metazoans and macrofaunal polychaete surveys. The latter was done by analyzing 11,466 individuals using a combination of morpho-taxonomy and DNA barcoding. Study objectives were to: (1) compare biotic signals associated with benthic impacts of salmon farming in the two data types; and (2) identify potential eDNA indicators to facilitate eDNA-based monitoring in Canada. Across both data types, alpha diversity parameters were reduced in sediments near fish cage edge and were negatively correlated with pore-water sulphide concentration. Presence/absence of known indicator taxon Capitella generally agreed well between the two methods despite that they differed in both the volume of sediment sampled and the molecular marker used. In eDNA data, there was a strong negative correlation between Nematoda OTU richness and pore-water sulphide concentration, and multiple approaches were used to identify OTUs related to organic enrichment statuses. We demonstrate that eDNA metabarcoding generates biotic signals that could be leveraged for environmental assessment of benthic impacts of fish farms in multiple ways: both alpha diversity and Nematoda OTU richness could be used to assess the spatial extent of impact, and OTUs related to organic enrichment could be used to develop a local biotic index.