The ecosystem concept has been applied to coral reefs since the time o
f Charles Darwin, perhaps because of the apparent integrity of the bio
tic-abiotic nexus. The modern model of the ecosystem as a hierarchy wi
th emergent properties is exemplified in reefs as massive structures f
ormed by small colonial organisms, the self-similarity of these struct
ures across large spatial scales, and the uniformity of function by di
verse biological communities. Emergent properties arise through the in
tegration of processes up the levels of organization and larger spatia
l and temporal scales encompassed by a whole reef. The organic respons
e of reef morphology to hydrodynamic forcing, the constancy and conser
vatism of organic production across a broad range of environments, and
the global persistence of reefs in the face of massive evolutionary c
hange in species diversity are interpreted as emergent properties. Cor
al reefs, of course, function by the same basic laws as other ecosyste
ms, but there is cause to view them as an end member of a continuum be
cause of their structural complexity and high internal cycling. Well-d
efined boundary conditions mean that highly integrative measures of ec
osystem process based on physical and biogeochemical models (e.g. comm
unity metabolism) have provided the main applications of systems ecolo
gy to questions of coral reef function. Organism-population approaches
are being reconciled with form-functional models to yield new insight
s to ecosystem processes and interactions among reefs and adjacent sys
tems. The form and metabolism of reef production are strongly affected
by phase shifts in benthic community structure, and most reef systems
are more open to trans-boundary fluxes and external forcing than the
early models suggest. The attractive paradigm of the reef as a self-su
fficient ecosystem is dying slowly as research focus shifts from atoll
s to more open fringing and bank barrier reefs, and organic inputs to
system production are measured. Coral reefs contribute little in a net
sense to global ecosystem processes, but on an areal basis their expo
rts of organic products are significant. Holistic models and measures
of ecosystem processes incorporate the unusual whole-part relationship
of reefs and are practically essential to answering the key questions
facing coral reef science in the next millennium.