Regional differences in trophic structure and availability of alternate sources of basal organic matter to food webs can affect the volume of organic matter converted into fish biomass. The present study combined stable isotope analyses (δ 13 C and δ 15 N) with estimates of biomass density of 22 common reef fishes to compare supply of organic matter derived from macroalgae versus phytoplankton to reef fish communities among 30 sites distributed across Fiordland and the Marlborough Sounds, 2 contrasting regions in terms of land-based stressors on the South Island, New Zealand. Fish communities in the Marlborough Sounds were supported by food webs that incorporated less organic matter derived from macroalgae compared to those in Fiordland. Contribution of organic matter derived from macroalgae to fish biomass decreased with trophic level in the Marlborough Sounds, while fishes in Fiordland were supported by a more equal mixture of organic matter derived from phytoplankton and macroalgae among trophic levels. Total fish biomass density was 1.72 times higher in Fiordland, yet the fish community converted 2.91 times more organ ic matter to fish biomass, as a result of a higher proportion of biomass at high trophic levels. The observed patterns were consistent with limitation in supply of organic matter derived from macroalgae in the Marlborough Sounds, where extensive losses of kelp forest habitat linked to land-based stressors have been reported. The results highlight the importance of considering regional variability in basal organic matter source pools, particularly those produced from sensitive kelp forest habitats, when applying ecosystem-based approaches to managing coastal resources.

1. The relative availability of alternative organic matter sources directly influences trophic interactions within ecological communities. As differences in trophic ecology can alter the productivity of communities, understanding spatial variability in trophic structure, and the drivers of variability, is vital for implementing effective ecosystem-based management.2. Bulk stable isotope analysis (δ 13 C and δ 15 N) and mass balance calculations were used to examine patterns in the contribution of organic matter derived from macroalgae to food webs supporting temperate reef fish communities in two contrasting coastal waterways on the South Island of New Zealand: Fiordland and the Marlborough Sounds. Ten fish species common to both regions were compared, with up to 40% less organic matter from macroalgae supporting omnivorous species in the Marlborough Sounds. The largest differences in trophic position were found in those species exploited by fisheries.3. Furthermore, stratified surveys of abundance and species biomass combined with trophic position data were used to calculate regional differences in the contribution of macroalgae to whole fish communities in terms of density of biomass. In Fiordland, over 77% of the biomass of exploited reef fishes was supported by macroalgae, compared with 31% in the Marlborough Sounds. 4. Surveys of macroalgal density and species composition in the two regions indicated that regional differences in trophodynamics may be explained by a lack of macroalgal inputs to the food web in the Marlborough Sounds.5. The findings demonstrate large regional differences in the incorporation of benthic and pelagic sources of organic matter to food webs supporting reef fish communities, highlighting the need for ecosystem-based approaches to management to recognize spatial variability in primary production supporting coastal food webs.

On temperate rocky reefs, overexploitation of high‐trophic‐level omnivores can result in the decimation of kelp forest habitats by releasing sea urchin population networks from top‐down control. However, the local dynamics of the resulting trophic cascades are context‐dependent. Here, we investigate the community‐wide patterns associated with both diffuse stressors and localized protection of high‐trophic‐level omnivores in kelp forest ecosystems by comparing communities among marine reserves and fished areas in two contrasting regions in terms of fishing intensity and land‐based stressors, Fiordland and the Marlborough Sounds, New Zealand. We find higher densities of the potential sea urchin predators, red rock lobsters (Jasus edwardsii) and banded wrasse (Notolabrus fucicola), in the Fiordland region, and larger effect sizes of fishing on the exploited fish communities in the Marlborough Sounds. Patterns in sea urchin density were consistent with the idea that high‐trophic‐level species, such as large fish and rock lobsters, regulate sea urchin population density, with lower densities of Evechinus chloroticus observed inside marine reserves, in both regions. Nevertheless, densities of E. chloroticus were generally high (>3 m2) in the Marlborough Sounds, likely above a grazing threshold in both fished and reserve sites. The proportion of habitat where sea urchins were absent was 29% in Marlborough Sounds and 90% in Fiordland. Consequently, we observe 49% barren habitat in Fiordland vs. 70%, and a larger effect of fishing on kelp community structure, in the Marlborough Sounds, where fishing effect sizes and land‐based stressors were more severe. We propose that a combination of diffuse stressors including regional overexploitation of important sea urchin predators, sedimentation, and warming of coastal waters likely contributed to regional differences in the responses of trophic interaction chains to localized reductions in fishing within marine reserves. The present study highlights how physiologically stressed and modified kelp forest ecosystems are more susceptible to detrimental phase shifts at a regional spatial scale.

Fluxes of nutrients and organic matter between estuaries and the open coast comprise an important component of ecosystem connectivity. Nevertheless, relatively little is known about how oceanographic processes, for example onshore retention of water in the coastal boundary layer, interact with major sinks for particulate organic matter such as bivalve filter feeding within inlets and estuaries. To investigate this interaction, total fluxes of water, nutrients (NH4, NOx and PO4) and chlorophyll a between Waitati Inlet on the wave-exposed coast of the South Island, New Zealand, and the coastal ocean were quantified over 40 tidal cycles. We found declines in total flux of phytoplankton and increases in flux of NH4 between flood and ebb tides. Net declines in phytoplankton biomass followed a Type II functional response curve, consistent with consumption by the large biomass of filter feeding bivalves within the inlet; however, an asymptote was not reached for the highest concentrations, indicating that feeding was likely limited by exposure time rather than concentration of food relative to biomass. An information-theoretic framework was then used to infer the most likely combination of environmental conditions influencing total fluxes of phytoplankton into the inlet. Onshore wind stress, wave transport and salinity explained 90% of the variation in flux of phytoplankton entering the inlet on flood tides. These results highlight the importance of the interaction between oceanographic forcing and bivalve filter feeding in modulating material dynamics and connectivity between estuaries and the coastal ocean.