Producing coral reef benthic habitat maps from acoustic backscatter has been hindered by uncertainties in interpreting the acoustic energy parameters E1 (roughness) and E2 (hardness), typically limiting such maps to sediment classification schemes. In this study acoustic interpretation was guided by high-resolution LADS (Laser Airborne Depth Sounder) bathymetry. The acoustic survey was conducted in Palm Beach County, FL, from inshore sand to outer reef slope, using a multiplexed echosounder (BioSonics DT-X at 38 & 418 kHz). E1 and E2 values, empirically normalized to mean depth, were compared to spatially-coincident values of a LADS-derived proxy for topographic complexity (Reef-Volume) and eight LADS=delineated benthic habitat classes. The 38 and 418 kHZ E1 parameters were positively correlated with Reef-Volume, in agreement with the general empirical basis for bottom seabed classification. The opposite trend was observed for the 38 and 418 kHz E2 parameters, contrary to convention, which would predict an increasing trend of E2 from sand (soft, flat) to colonized pavement (hard, flat). Tukey HSD testing proved all four acoustic parameters capable of distinguishing between habitats; significant differences ranged from 25-27 of the k(k-1)/2 = 28 comparisons between the eight habitat categories. An a posteriori discriminant analysis of each frequency, paring E1 and E2 as predictor variables, showed that the 418 kHz signal provided superior predictive accuracy for six (consolidated from eight) habitat classes (74.3 versus 68.2%). Consideration of all results reveals topographic complexity as the primary factor controlling both E1 and E2. The information encoded in the two frequencies is generally the same, with 418 kHz being better suited for discriminating between habitats of high complexity and 38 kHz for distinguishing between sand and sand-over-hardbottom. The LADS bathymetry proved useful for demonstrating the E1 and E2 values of single-beam echosounders can indeed produce meaningful coral reef benthic habitat maps.