In recent years, new multibeam echosounders that can simultaneously collect data at multiple frequencies have become available. However, the effects of acoustic frequency on bathymetric data have yet to be characterized, as early research on these new systems has instead focused on backscatter data. Here we explore such effects by deriving terrain attributes and classifications from bathymetric data from Head Harbour, Nova Scotia, Canada, that were collected at five different operating frequencies. The geomorphometric analyses were conducted on bathymetric surfaces generated from data collected at each operating frequency using four scales of analysis. Results show that bathymetry, its derived terrain attributes, and terrain classifications produced with them are all dependent on the acoustic frequency used to collect bathymetric data. While the observed effects on the regional bathymetry were relatively minor, local bathymetry, terrain attributes and terrain classifications were highly impacted by the frequency used when collecting data. The impacts were less important when the terrain attributes and classifications were generated using broader scales of analysis. These results raise questions about how bathymetry is measured and defined and how we should interpret the outcomes of marine geomorphometric analyses. This is particularly relevant as such analyses have become a key component of marine habitat mapping and submarine geomorphology mapping.