Human populations and economic activity are increasingly skewed towards the coast (Hinrichsen 1999). Three-quarters of all large cities are located on the coast (Tibbetts 2002), 40% of the global population live within 100 km of the coast, and 90% of global trade occurs by sea (IMO 2012). The centres of people and trade, and the areas that must adapt the fastest to support societal demands, are our ports and harbours. It is in these places where both the world’s wealth and the world’s population are concentrated (Hinrichsen 1999). In the US alone, 21 million peoplemove to the coastal counties every year. In China, 60% of the nation’s 1.2 billion people live in 12 coastal provinces. Some countries are already almost entirely coastal, such as Vietnam, Bangladesh, Australia, Japan and the Philippines (Hinrichsen 1999). Even Africa, the only continent where there are more people living inland than near the coastline, is witnessing a rapid coastal transition. This movement is driven by work opportunities that are concentrated in urban areas. In addition, climatic changes and agricultural change legacies render inland areas less hospitable, aggravating the exodus to coastal zones (Tibbetts 2002). With burgeoning populations and the growth of economic development of coastal areas has come substantial change and development. Unfortunately, in many countries we now have a substantial legacy of environmental impact and there is a scarcity of political motivation, expertise or money to plan and implement comprehensive coastal conservation and management plans (Hinrichsen 1999; Li 2003). This, combined with a lack of understanding of the full implications of these demographic and resource trends, results in ports and harbours around the globe being subjected to myriad ongoing stressors. These issues are not specific to any one nation, region or city. Coastal communities worldwide are facing the same problems (Tibbetts 2002). Artificial structures such as ports, pilings and seawalls have replaced much of the natural shoreline reducing native biodiversity (Bulleri and Chapman 2010) and land has been reclaimed changing the hydrodynamics of the waterways (e.g. Suh et al. 2014). Contaminants exist as legacies of industrial waste disposal practices rendering local seafood toxic to consumers and diffuse inputs from concretised catchments cause ongoingwater quality problems alongside the degradation of marine vegetation (Kennish 1997; Birch 2000). Shipping activities bring many non-indigenous species that may be acting to homogenise port biota into a single, global, species pool (Ruiz et al. 1997). All this has caused much damage to our waterways and the question becomes – can we recover, restore, re-use or retrofit? Can we transform these places of industry and trade, to places that facilitate multiple uses and values including recreation and biotic diversity? Can we restore damaged ecosystems and the services they provide? There is an urgent need to take stock of the current biophysical state of port and harbour ecosystems and the threats they are facing. We must do this so we can make better predictions and decisions for the future. Knowledge can inform our path, but only if it is remembered, synthesised, translated and embedded into policy and regulation. Current understandings from multiple fields of research must be gathered together, and built into frameworks for decision-making (Wooldridge et al. 1999). Identifying the status and threats to ecological components and processes is the crucial first step in this process that underpins ecological risk analyses and the establishment of management strategies with integrated monitoring programs (Burgman 2005). In this edition of Marine and Freshwater Research we present two major reviews of what is possibly the world’s most biologically diverse port. Sydney Harbour is renowned for its natural beauty, emanating from a complex series of natural embayments and rocky headlands. The estuary sits at the heart of a vast urban metropolis, home to almost 5 million people. But for too long, we have accepted a patchwork approach to managing its natural resources. The lack of cooperation and synthesis is surprising given how important the Harbour is to the commercial and social prosperity of the city, the region and the nation more generally. This is the first systematic review of published biophysical information on Sydney Harbour and pulls together, not only a comprehensive assessment of its habitats, diversity and ecosystem functioning (Johnston et al. 2015), but also a detailed inventory and interpretation of threats and stressors (Mayer-Pinto et al. 2015). Sydney Harbour is a drowned river valley; carved into Hawkesbury sandstone some 25–29 million years ago and filled by a rising sea 17 000–6000 years ago (Roy 1981). CSIRO PUBLISHING