The Ningaloo Marine Park is situated on the mid-west coast of Australia and incorporates approximately 300km of tropical/sub-tropical fringing reef system. Originally gazetted in 1987, the park is a popular recreational location that has received steadily increasing visitation over the past two decades. Recreational fishing is one of the most common user activities, with spatial zoning and bag limits being the primary management strategies for the conservation of fish communities. However, despite the relatively large spatial coverage of no-take areas (NTA’s; ~34% of the total area) and the length of time in which they have been in place (9-29 years), meta-analysis of surveys conducted over the past 29 years indicates that there has been no change in the effect size of NTA’s on highly targeted fish communities through time. While the vast majority of surveys indicate higher target species abundance within NTA’s, data collected at high use areas provides evidence for steady declines in the abundance of the primarily targeted fish group (Lethrinidae) both inside and outside of these protected areas. Here we investigate the potential causes of these patterns including the influence of fishing intensity, non-compliance, benthic habitat, reef zone, zoning design and recruitment supply. We scrutinise evidence to support each of these factors and conclude that it is a combination of many of the aforementioned aspects influencing the abundance of target fish groups. Our results highlight the complex nature of drivers of marine populations and the need to consider multiple factors when assessing the efficacy of conservation and marine protected area management strategies.