Predicting and abating the loss of natural habitats present a huge challenge in science, conservation and management. Algal forests are globally threatened by loss and severe recruitment failure, but our understanding of resilience in these systems and its potential disruption by anthropogenic factors lags well behind other habitats. We tested hypotheses regarding triggers for decline and recovery potential in subtidal forests of canopy-forming algae of the genus Cystoseira.By using a combination of historical data, and quantitative in situ observations of natural recruitment patterns we suggest that recent declines of forests along the coasts of the north Adriatic Sea were triggered by increasing cumulative impacts of natural- and human-induced habitat instability along with several extreme storm events. Clearing and transplantation experiments subsequently demonstrated that at such advanced stages of ecosystem degradation, increased substratum stability would be essential but not sufficient to reverse the loss, and that for recovery to occur removal of the new dominant space occupiers (i.e., opportunistic species including turf algae and mussels) would be required. Lack of surrounding adult canopies did not seem to impair the potential for assisted recovery, suggesting that in these systems recovery could be actively enhanced even following severe depletions.We demonstrate that sudden habitat loss can be facilitated by long term changes in the biotic and abiotic conditions in the system, that erode the ability of natural ecosystems to absorb and recover from multiple stressors of natural and human origin. Moreover, we demonstrate that the mere restoration of environmental conditions preceding a loss, if possible, may be insufficient for ecosystem restoration, and is scarcely cost-effective. We conclude that the loss of complex marine habitats in human-dominated landscapes could be mitigated with appropriate consideration and management of incremental habitat changes and of attributes facilitating system recovery.