Baited Underwater Video (BUV) systems have become increasingly popular for assessing marine biodiversity. These systems provide video footage from which biologists can identify the individual fish species present. Here we explore the relevance of spatial dependence and marine park boundaries while estimating the distribution and habitat associations of the commercially and recreationally important snapper species Chrysophrys auratus in Moreton Bay Marine Park during a period when new Marine National Parks zoned as no-take or “green” areas (i.e., areas with no legal fishing) were introduced. BUV studies typically enforce a minimum distance among BUV sites, and then assume that observations from different sites are independent conditional on the measured covariates. In this study, we additionally incorporated the spatial dependence among BUV sites into the modelling framework. This modelling approach allowed us to test whether or not the incorporation of highly correlated environmental covariates or the geographic placement of BUV sites produced spatial dependence, which if unaccounted for could lead to model bias. We fitted Bayesian logistic models with and without spatial random effects to determine if the Marine National Park boundaries and available environmental covariates had an effect on snapper presence and habitat preference. Adding the spatial dependence component had little effect on the resulting model parameter estimates that emphasized positive association for particular coastal habitat types by snapper. Strong positive relationships between the presence of snapper and rock habitat, particularly rocky substrate composed of indurated freshwater sediments known as coffee rock, and kelp habitat reinforce the consideration of habitat availability in marine reserve design and the design of any associated monitoring programs.