Historic baselines are important in developing our understanding of ecosystems in the face of rapid global change. While a number of studies have sought to determine changes in extent of exploited habitats over historic timescales, few have quantified such changes prior to late twentieth century baselines. Here, we present, to our knowledge, the first ever large-scale quantitative assessment of the extent and biomass of marine habitat-forming species over a 100-year time frame. We examined records of wild native oyster abundance in the United States from a historic, yet already exploited, baseline between 1878 and 1935 (predominantly 1885–1915), and a current baseline between 1968 and 2010 (predominantly 2000–2010). We quantified the extent of oyster grounds in 39 estuaries historically and 51 estuaries from recent times. Data from 24 estuaries allowed comparison of historic to present extent and biomass. We found evidence for a 64 per cent decline in the spatial extent of oyster habitat and an 88 per cent decline in oyster biomass over time. The difference between these two numbers illustrates that current areal extent measures may be masking significant loss of habitat through degradation.

The oyster habitat in the USA is a valuable resource that has suffered significant declines over the past century. While this loss of habitat is well documented, the loss of associated ecosystem services remains poorly quantified. Meanwhile, ecosystem service recovery has become a major impetus for restoration. Here we propose a model for estimating the volume of water filtered by oyster populations under field conditions and make estimates of the contribution of past (c. 1880–1910) and present (c. 2000–2010) oyster populations to improving water quality in 13 US estuaries. We find that filtration capacity of oysters has declined almost universally (12 of the 13 estuaries examined) by a median of 85 %. Whereas historically, oyster populations achieved full estuary filtration (filtering a volume equivalent or larger than the entire estuary volume within the residence time of the water) in six of the eight estuaries in the Gulf of Mexico during summer months, this is now the case for only one estuary: Apalachicola Bay, Florida. By contrast, while all five estuaries on the North Atlantic coast showed large decreases in filtration capacity, none were achieving full estuary filtration at the time of our c. 1900 historic baseline. This apparent difference from the Gulf of Mexico is explained at least in part by our North Atlantic baseline representing a shifted baseline, as surveyed populations were already much reduced by exploitation in this region.

Summary: Quantification of ecosystem services is increasingly valuable for conservation and restoration decision‐making. Structured habitats serve as nursery grounds by enhancing juvenile fish and mobile crustacean survival and abundance. This service is challenging to quantify due to ontogenetic shifts in habitat use by many species. We reviewed available literature on the increased abundance of juvenile fish and mobile crustaceans in a key nursery habitat – Crassostrea virginica reefs in the USA. We modelled the growth and mortality of the enhanced species using three different natural mortality (M) estimates to provide estimates of the gross and net lifetime production and uncertainty that can be attributed to the habitat. Recruitment of nineteen and twelve species were found to be enhanced by the addition of C. virginica reefs to previously unstructured habitat in the Gulf of Mexico and the South Atlantic and Mid‐Atlantic USA, respectively. This increased recruitment is estimated to result in a mean lifetime enhancement in production of 397 ± 115 (1 SD) g m⁻² year⁻¹ in the Gulf of Mexico and 281 ± 56 g m⁻² year⁻¹ in the South Atlantic and Mid‐Atlantic. The two regions differed with regard to the identity of the enhanced species and their degree of augmentation. Thus, our results highlight the inadequacy of applying regional estimates of ecosystem services to global scales. Furthermore, estimates of total enhancement varied by up to a factor of 2·8 across the three methods of M estimation. Our estimates are quantitative predictions of the ecological benefits derived from the restoration or conservation of a threatened habitat, and advance the field of restoration science beyond qualitative statements that just predict direction of benefit (e.g. increased or decreased). Quantification of the uncertainty in the production estimates further increases their utility for decision‐makers. Synthesis and applications. Our results can be applied to the restoration or conservation of nursery habitats where habitat is limiting the recruitment of fish species. Quantitative estimates of fisheries productivity enhancement by habitats can be used by managers to determine the expected return on investment in restoration activities, provide testable predictions for monitoring programs and communicate the value of restoring or conserving habitat.

Widespread global declines in shellfish reefs (ecosystem‐forming bivalves such as oysters and mussels) have led to growing interest in their restoration and protection. With restoration projects now occurring on four continents and in at least seven countries, global restoration guidelines for these ecosystems have been developed based on experience over the past two decades. The following key elements of the guidelines are outlined: (a) the case for shellfish reef restoration and securing financial resources; (b) planning, feasibility, and goal setting; (c) biosecurity and permitting; (d) restoration in practice; (e) scaling up from pilot to larger scale restoration, (f) monitoring, (g) restoration beyond oyster reefs (specifically mussels), and (h) successful communication for shellfish reef restoration projects.