1. The world's coral reefs are under threat as climate change causes increases in frequency and severity of acute thermal stress. This is compounded by chronic pressures including rises in sea surface temperature, overfishing and decline in water quality. Monitoring to understand the recovery dynamics of corals is paramount to enable effective management of coral reefs. While detailed mechanistic models provide insight into reef recovery patterns, colony scale monitoring is not viable for reefs over a large geographical extent, such as the Great Barrier Reef (GBR). Consequently, aggregated coral cover data are utilised in practice and phenomenological analysis directly applicable to these monitoring programmes is essential for reef health reporting. These analyses are especially challenging for assessment of recovery potential of reefs reduced to very low coral cover (<10%) after disturbance since standard modelling assumptions may not hold.2. Through the application of an innovative diagnostic approach modified from methods used in cancer cell biology, we found that almost 50% of reefs recovering from low cover exhibited a previously undocumented initial phase of slower growth per unit cover before sigmoid coral cover recovery trajectories were observed. Without properly accounting for these reduced growth periods, the expected performance of reefs may be overestimated immediately after disturbance events.3. The presence of two-phase recovery patterns has a profound negative impact on the continued provision of ecological services from these reefs as major disturbance frequencies increase. Projections show that if the time between major disturbances is <5 years, then reefs with two-phase growth are never likely to reach 15% cover. Synthesis and applications.This work provides a method to detect two-phase recovery, the tendency for observed reef recovery to be slower than expected after a major disturbance. This phenomenon is observed across the Great Barrier Reef with serious implications for recovery potential as major disturbances occur more frequently due to climate change. Identification of reefs prone to two-phase recovery can assist the triage of reefs for intervention actions in response to

Macroalgae are an important component of coral reef ecosystems. We identified spatial patterns, environmental drivers and long-term trends of total cover of upright fleshy and calcareous coral reef inhabiting macroalgae in the Great Barrier Reef. The spatial study comprised of one-off surveys of 1257 sites (latitude 11–24°S, coastal to offshore, 0–18 m depth), while the temporal trends analysis was based on 26 years of long-term monitoring data from 93 reefs. Environmental predictors were obtained from in situ data and from the coupled hydrodynamic-biochemical model eReefs. Macroalgae dominated the benthos (≥50% cover) on at least one site of 40.4% of surveyed inshore reefs. Spatially, macroalgal cover increased steeply towards the coast, with latitude away from the equator, and towards shallow (≤3 m) depth. Environmental conditions associated with macroalgal dominance were: high tidal range, wave exposure and irradiance, and low aragonite saturation state, Secchi depth, total alkalinity and temperature. Evidence of space competition between macroalgal cover and hard coral cover was restricted to shallow inshore sites. Temporally, macroalgal cover on inshore and mid-shelf reefs showed some fluctuations, but unlike hard corals they showed no systematic trends. Our extensive empirical data may serve to parameterize ecosystem models, and to refine reef condition indices based on macroalgal data for Pacific coral reefs.