Dual-frequency identification sonar (DIDSON) offers important advantages over other sampling tools for observing pelagic and benthic fishes in situ. Because it relies on sound, DIDSON can detect fish in a non-destructive and non-intrusive manner. In our unique application, the equipment's small size and low power requirements allow deployment from a kayak for increased maneuverability in complex habitats. Characteristics that typify echograms of different fishes can be extracted using multivariate ordination techniques, such as principal components analysis (PCA), with in situ groundtruthing. Here we present reference images, techniques, and human-observer-error estimates from DIDSON application. Together, these approaches enhance our ability to sample fishes and even observe certain behaviors in complex, turbid environments during a full diel cycle.