Aim Marine reef habitats are typically defined subjectively. We provide a continental‐scale assessment of dominant reef habitats through analysis of macroalgae and sessile animal taxa at sites distributed around Australia. Relationships between reef habitats and environmental and anthropogenic factors are assessed, and potential changes in the future distribution and persistence of habitats are considered. Location Shallow rocky and coral reefs around the Australian coast. Methods Cover of 38 sessile biota functional groups was recorded in diver‐based surveys using quadrats at 1,299 sites. Classification analyses based on the functional groups were used to identify an unambiguous set of ‘biogenic habitat types’. Random forest and distance‐based linear modelling were used to investigate correlations between these habitats and environmental and anthropogenic variables. Results Cluster analyses revealed tropical and temperate ‘realms’ in benthic substratum composition, each with finer‐scale habitats: four for the temperate realm (canopy algae, barren, epiphytic algae–understorey and turf) and five for the tropical realm (coral, coral–bacterial mat, turf–coral, calcified algae–coral and foliose algae). Habitats were correlated with different sets of environmental and anthropogenic conditions, with key associations in the temperate realm between mean sea temperature and canopy‐forming algae (negative) and barren habitat (positive). Variation in sea temperature was also an important correlate in the tropical realm. Main conclusions Quantitative delineation of inshore reef habitats at a continental scale identifies many of the same habitat types traditionally recognized through subjective methods. Importantly, many biogenic reef habitats were closely related to environmental parameters and anthropogenic variables that are predicted to change. Consequently, habitats have differing likelihood of persistence. Structurally complex habitats in the temperate realm are at greater risk than more ‘two‐dimensional’ habitats (e.g., canopy‐forming versus turfing algae). In the tropical realm, offshore and coastal habitats differed greatly, highlighting the importance of large‐scale oceanic conditions in shaping biogenic structure.

While there are numerous studies that have used no-take marine reserves (NTMRs) to understand the effects of commercial fishing, much less is known about the influence of NTMRs in regions subject to recreational fishing. We used meta-analysis to synthesise data from 4,444 samples from 30 years (1987-2017) of fish 7 surveys, inside and outside a large network of NTMRs in the Ningaloo Marine Park, Western Australia, 8 where the major fishing activities are recreational. The data were collected by different agencies, using 9 varied survey designs and sampling methods. We contrasted the relative abundance and biomass of target 10 and non-target fish groups between fished and NTMR locations. We considered the influence of, and 11 possible interactions between, seven additional variables: age and size of NTMR, one of two reserve network configurations, reef habitat type, the level of recreational fishing activity, shore-based fishing regulations and survey method. Taxa responded differently: commonly targeted lethrinids had clear higher average abundance and biomass inside NTMRs, while the abundance/biomass of other targeted (and nontargeted groups) were indistinguishable inside to outside. Reef habitat was an important factor governing lethrinid response to protection, and we showed this variable can interact with reserve size, with larger NTMRs only demonstrably more effective than smaller ones in the back reef/lagoon habitats. There was little evidence of changes in relative abundance/biomass with reserve age, or before and after rezoning and expansion of the NTMR network. Our study demonstrates the complexity of fish responses to protection and fishing, and also highlights some of the key factors and interactions that likely underlie the varied results found to date in NTMR assessments, and that should thus be considered in future reserve design and 22 assessment. 23 24 Keywords 25 Marine protected area; MPA; fisheries; coral reef; Ningaloo; adaptive management; recreational fishing; Lethrinus 1. Introduction Anthropogenic activities continue to expand worldwide, particularly in the tropics, threatening natural systems and the ecosystem services they provide (Barlow et al. 2018). As a result, 'protected areas' that seek 32 to balance extractive activities with other socio-ecological values are increasingly being used to manage 33 terrestrial and marine systems (Jenkins & Joppa 2009; Sala et al. 2018). Many studies have assessed the conservation effects of no-take marine reserves (NTMR) (reviewed by Mosquera et al. 2000; Russ 2002), including quantitative syntheses of regional and global studies, with most finding higher abundance and size of targeted species within reserve boundaries (Lester et al. 2009). The large majority of these findings are from regions with commercial fisheries operating, and less is documented about the impacts of recreational fisheries, despite several studies flagging the potentially high impacts of these fisheries (McPhee et al. 2002; Coleman et al. 2004; Cowx & Cooke 2004; Lewin et al. 2...

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