Differences in the reef biota between the Point Labatt Marine Reserve and adjacent unprotected reference areas were examined following an 18-year period of protection from fishing. Quantitative measures of fish, invertebrates and algae were obtained by divers at 16 depth-stratified locations inside and outside the reserve, and the significance of differences examined using a combination of univariate (ANOVA) and multivariate (MDS) analyses. Strong depth-related differences in the composition and abundance of algae and invertebrates were observed, both inside and outside the reserve. These community differences were most pronounced in shallow near-shore waters (<10 m depth), and were largely due to variations in the abundance of a small group of species with widespread distributions. Spatial patterns in fish were not closely related to depth, and it appears that trophic linkages between fish and the underlying algal and invertebrate assemblages at Point Labatt are either weak or occur at spatial scales larger than that covered in this study. No significant reserve-related differences were detected in the abundance, diversity or community structures of algae, invertebrates and fish examined in this study. In many cases this is because the biological attributes measured were highly variable in space, and required more intensive sampling regimes to improve statistical precision. This study emphasizes the need for more robust survey designs and their timely implementation in marine conservation planning processes.