The density of human populations in nearshore areas is more than three times the global average and is one example of why monitoring sensitive nearshore environments is essential. In this paper we outline a method for map-based monitoring of nearshore flora and epifauna using the seabed imaging and mapping system (SIMS) and geographic analysis. This system uses underwater video and sidescan sonar to systematically inventory and classify nearshore habitats. Species presence and abundance were mapped in 2006 and 2009 for a coastal area of British Columbia, Canada, and represented in a geographic information system (GIS). Spatial statistics were applied to maps of change in species abundance, and hot spots of floral and epifaunal change were identified. While minimal overall change within species groups occurs over 3 years, local areas of significant change were found near the marina entrance and the Washington State ferry terminal, where marine boat traffic may be affecting vegetation. The use of spatial statistics with this method reduces the effects of seasonal variability, minimizes impact of data errors, and identifies statistically significant hot spots of change. We have also demonstrated that SIMS generates suitable data for change detection and monitoring.