Tidal flooding occurs when coastal water levels exceed impact-based flood thresholds due to tides alone, under average weather conditions. Transitions to tidal flood regimes are already underway for nuisance flood severities in harbours and bays and expected for higher severities in coming decades. In the first such regional assessment, we show that the same transition to tidally forced floods can also be expected to occur in Australian estuaries with less than 0.1 m further sea-level rise. Flood thresholds that historically used to only be exceeded under the combined effects of riverine (freshwater) and coastal (salt water) influences will then occur due to high tides alone. Once this tidal flooding emerges, it is projected to become chronic within two decades. Locations most at-risk of the emergence of tidal flooding and subsequent establishment of chronic flood regimes are those just inside estuary entrances. These locations are exemplified by low freeboard, the vertical distance between a flood threshold and a typical high tide level. We use a freeboard-based analysis to estimate the sea-level rise required for impacts associated with official flood thresholds to occur due to tides alone. The resultant tide-only flood frequency estimates provide a lower bound for future flood rates.

Applying a coastal-geoarchaeological approach, we synthesize stratigraphic, sedimentological, mollusk-zooarchaeological, and radiometric datasets from recent excavations and sediment coring at Harbor Key (8MA15)—a shell-terraformed Native mound complex within Tampa Bay, on the central peninsular Gulf Coast of Florida. We significantly revise the chronological understanding of the site and place it among the relatively few early civic-ceremonial centers in the region. Analyses of submound contexts revealed that the early first millennium mound center was constructed atop a platform of sand and ex situ cultural shell deposits that were reworked during ancient storm landfalls around 2000 BP. We situate Harbor Key within a seascape-scale stratigraphic and paleoenvironmental framework and show that the shellworks comprise an artificial barrier protecting the leeward estuary basin (and productive inshore wetlands) from high-energy conditions of the open bay and swells from the Gulf of Mexico. The sedimentary and archaeological records attest to the long-term history of morphodynamic interaction between coastal processes and Indigenous shell terraforming in the region and suggest that early first millennium mound building in Tampa Bay was tied to the recognition and reuse of antecedent shellworks and the persistent management of encompassing cultural seascapes.

Ficopomatus Southern, 1921 is a serpulid genus currently composed of six species, two of which (F. enigmaticus and F. miamiensis) are reef-builders. The former has invaded subtropical and warm-temperate estuaries worldwide, causing environmental and economic harm. In this study, Ficopomatus miamiensis and F. uschakovi are reported from brackish-water coastal localities in both Atlantic and Pacific sides of Mexico, including a Biosphere Reserve, estuaries, as well as shrimp and oyster farms. Ficopomatus miamiensis is reported from Veracruz (southern Gulf of Mexico, Mexico territory) and Sinaloa (southern Gulf of California). Ficopomatus uschakovi is reported for the first time in the southern Gulf of Mexico (Mexico territory) and repeatedly recorded in Chiapas (southern Mexican Pacific). There are no phenotypic differences between specimens of F. miamiensis from both coasts of Mexico. Comparison of mitochondrial cytochrome b (Cytb) DNA sequences further support the notion that F. miamiensis from the type locality (Florida) and Atlantic coasts of Mexico is also found along the Pacific coast of Mexico. Morphological variability within specimens of F. uschakovi from a single locality (either Laguna del Ostión or La Encrucijada) in Mexico suggest potential presence of multiple cryptic species. Molecular genetics studies are needed to confirm the taxonomic and invasive status of F. uschakovi.

Otoliths are an excellent tool in studies on ecological connectivity of fish species populations. Opsanus beta is an invasive species introduced on the Brazilian coast, but not native from the Gulf of Mexico. The present study aimed to compare the otolith contours of specimens collected in Mexico (Celestún, CEL) and in two Brazilian estuaries (Santos Bay, STB, and Paranaguá Estuarine Complex, PEC). In the laboratory, 99 otoliths were extracted, photographed and compared using wavelet analysis. The otolith contours varied between sites (39 from CEL, 26 from STB and 34 from PEC). The linear discriminant analysis correctly reclassified 87.9% of otoliths by sites, with the best reclassifications in the CEL (97.36%), followed by PEC (88.23%) and SBT (73.07%). MANOVA showed significant differences in otolith contours between sites (F = 5.37; P < 0.005). The otolith contour from CEL was significantly different from those from the PEC and SBT. However, the otolith contour of the two Brazilian estuaries did not significantly differ among them (MANOVA, P > 0.005). Our results indicate O. beta populations on the Brazilian coast are connected, and probably isolated from the Mexican population.

Given the abundance, heterogeneity and ubiquity of parasitic organisms, understanding how they influence biodiversity, evolution, health and ecosystem functionality is crucial, especially currently when anthropogenic pressures are altering host–parasite balances. This review describes the features, roles and impacts of metazoan parasites of fish occurring in transitional waters (TW). These aquatic ecosystems are highly productive and widespread around the globe and represent most favourable theatres for parasitism given the availability of hosts (invertebrates, fishes and birds) and an increased probability of parasite transmission, especially of those having complex life cycles. Fascinating examples of how parasitism can influence different hierarchical levels of biological systems, from host individuals and populations to entire aquatic communities, through effects on food webs come from this kind of ecosystem. Edible fish of commercial value found in TW can harbour some parasite species, significantly reducing host health, marketability and food safety, with possible economic and public health consequences. Many TW are historically exploited by humans as sources of relevant ecosystem services, including fisheries and aquaculture, and they are highly vulnerable ecosystems. Alteration of TW can be revealed through the study of parasite communities, contributing, as bioindicators, for assessing environmental changes, health and restoration. Fish parasites can provide much information about TW, but this potential appears to be not fully exploited. More studies are necessary to quantify the ecological, economic and medical impacts fish parasites can have on these important ecosystems.

Flood and drought events cause significant freshwater inflow fluctuations in estuaries, potentially leading to physiological stress and altered abundances of pathogens such as Vibrio vulnificus and Perkinsus marinus in oysters. To assess the effects of freshwater pulses to oyster reefs in subtropical estuaries in Texas, this study accomplished two goals: 1) reconstructed a reef-specific history of freshwater pulses through shell stable isotope analysis, 2) quantified the abundance of V. vulnificus and P. marinus through culture-dependent and culture-independent microbiology analyses. Oysters from a low-relief and high-relief reef experienced similar fluctuations in shell isotopes, indicating similar ranges of past environmental conditions. V. vulnificus and P. marinus were detected throughout the study but the abundance of these microorganisms was not correlated with environmental parameters or one another. Importantly, the P. marinus infection intensity was always lower at the high-relief reef, which suggests that high-relief reefs may experience lower infection frequencies.

Estuaries are water bodies, many of which contribute to the sustainable development of cities. Many of them are considered natural landscapes, offering various recreational services to the population. However, estuary degradation is a common problem in developing countries. Ecuador, for example, has a significant problem with the pollution of its estuaries. Machala is one of the most affected cities due to the contamination of these water bodies. This issue has generated negative externalities in the housing market. Thus, our central hypothesis is that rental prices of houses are revalued as their distance from polluted estuaries increases. Using the hedonic pricing approach, our results confirm that the price of a residence increases by US$9.45 for every 100 m farther it is from the closest estuary. This amount constitutes approximately 5.25 per cent of the average rental value in Machala.

The mojarras (Eucinostomus) are a widespread group of coastal fishes of controversial taxonomy because of similarities in their external morphology. In the present study, we assessed the genetic diversity of species and populations of Eucinostomus using DNA barcodes using a systematic and phylogeographic context. In total, 416 COI sequences of all valid Eucinostomus representatives were analysed based on public databases and collected specimens from the north-eastern coast of Brazil (Western South Atlantic). Several cases of misidentification were detected in the barcode dataset (E. argenteus, E. harengulus, E. gula, E. dowii and E. jonesii) that could account for the taxonomic issues in this genus. In contrast, we identified four molecular operational taxonomic units (MOTUs), with divergence above 2% in the Western Atlantic, that correspond to cryptic forms within E. argenteus, E. harengulus, E. gula and E. melanopterus. These data suggest that Plio-Pleistocene events (rise of the Panama isthmus, Amazonas outflow and sea-level fluctuations) played a major role in the diversification of mojarras. While subtle morphological differences have been used as proxies to discriminate Eucinostomus species, the genetic data proved to be efficient in differentiating them and revealing potentially undescribed taxa. Therefore, we recommend that further taxonomic studies in mojarras should incorporate DNA-based evidence.

Rapidly accumulating Holocene sediments in estuaries commonly are difficult to sample and date. In Chesapeake Bay, we obtained sediment cores as much as 20 m in length and used numerous radiocarbon ages measured by accelerator mass spectrometry methods to provide the first detailed chronologies of Holocene sediment accumulation in the bay. Carbon in these sediments is a complex mixture of materials from a variety of sources. Analyses of different components of the sediments show that total organic carbon ages are largely unreliable, because much of the carbon (including coal) has been transported to the bay from upstream sources and is older than sediments in which it was deposited. Mollusk shells (clams, oysters) and foraminifera appear to give reliable results, although reworking and burrowing are potential problems. Analyses of museum specimens collected alive before atmospheric nuclear testing suggest that the standard reservoir correction for marine samples is appropriate for middle to lower Chesapeake Bay. The biogenic carbonate radiocarbon ages are compatible with 210Pb and 137Cs data and pollen stratigraphy from the same sites.

Post-settlement changes in sediment transport and accumulation is an important environmental issue in many estuaries, including the Chesapeake. Our data show that large variations in sediment mass accumulation rates occur among sites. At shallow water sites, local factors seem to control changes in accumulation rates with time. Our two relatively deep-water sites in the axial channel of the bay have different long-term average accumulation rates, but the history of sediment accumulation at these sites appears to reflect overall conditions in the bay. Mass accumulation rates at the two deep-water sites rapidly increased by about fourfold coincident with widespread land clearance for agriculture in the Chesapeake watershed.

Flooding of the southern part of the North Sea occurred between 9000 and 8000 BP, when the rate of relative sea-level rise was on the order of 0.7 cm per year for the Dover Strait Region and 1.6 cm per year for the area north of the Frisian Islands, forcing the shoreline to recede rapidly. When relative sea-level rise decelerated after 7000 BP for the Belgian coast and 6000 BP for the central Netherlands coast, sediment supply by the tidal currents balanced the creation of accommodation space in the estuaries and other back-barrier basins. Consequently, the barrier started to stabilize, and the tidal basins and their inlets silted up. Between 5500 and 4500 BP, the Belgian coastal plain changed into a freshwater marsh with peat accumulation, and the same happened 500–1000 years later in the western provinces of the Netherlands. The E-W running barrier/back-barrier system of the Frisian Islands in the northern Netherlands stayed open until today, however, because of lower sediment supply.

The period between 4000 and 2000 BP was relatively quiet due to the strong deceleration of the rate of sea-level rise; peat cushions developed behind the barriers, which were straightened by erosion of the headlands. Major and often catastrophic flooding occurred in the Middle Ages, when the estuaries in the southwestern part of the Netherlands formed.

About 226 (± 15%) × 109 m3 sediment, mostly sand, is stored in the barriers and back-barrier basins of the Netherlands, 70% of which was deposited prior to 5000 BP. About 10% of the stored sediment is estimated to be of alluvial origin. Most of the sediment is derived by the erosion of the Pleistocene basement during recession of the barriers, but tide-induced crossshore transport from the North Sea forms an additional source for the barriers and back-barriers of the west-facing coast of the Netherlands.

Reactive-transport models contribute significantly to the field of modern geosciences. A general mathematical approach to solving models of complex biogeochemical systems is introduced. It is argued that even though mathematical models for reactive-transport simulations can be developed at various levels of approximation, the approach for their construction and application to the various compartments of the hydrosphere is fundamentally the same. The workings of coupled transport-reaction systems are described in more detail by means of examples, which demonstrate the similarities in the approach. Three models of the carbon dynamics in redox-stratified environments are compared: porous media flow problems in a coastal sediment and in a contaminated groundwater system; and a surface flow problem in a eutrophic estuary. Considering the interdisciplinary nature of such models, a Knowledge Base System for biogeochemical processes is proposed. Incorporation of the proposed knowledge base in an appropriate modeling framework, such as the Biogeochemical Reaction Network Simulator, proves an effective approach to the modeling of complex natural systems. This methodology allows for construction of multi-component reactive-transport models applicable to a wide range of problems of interest to the geoscientist.

Soft bottom intertidals of the Atlantic SW are dominated by the semi-terrestrial crab Neohelice granulata and the grapsid crab Cyrtograpsus angulatus. They are similar in size but C. angulatus is mainly a subtidal species, while N. granulata inhabits the intertidal zones, thus the two species overlap only during high tides in this area. Since these distribution differences between crab species across the Mar Chiquita Coastal lagoon may affect digenean infection success, the objective of this work is to describe the spatial differences in parasite infection levels and their selectivity on the host. To determine possible spatial differences in parasitism levels between sites and crab species across the lagoon, three areas dominated by N. granulata were selected and adult crabs of N. granulata and C. angulatus were collected. Both crab species harboured metacercariae of the digeneans Microphallus szidati and Maritrema bonaerensis (Microphallidae), and cystacanths of the acanthocephalan Profilicollis chasmagnathi (Profilicollidae). Digenean species showed preferences between the two crabs. Maritrema bonaerensis mean intensity was higher in N. granulata than in C. angulatus, while the opposite trend was found for M. szidati and could indicate some level of specificity. These results, nevertheless, depended on the study site. For P. chasmagnathi the highest values of mean intensity depended more on the site than on the crab species. The values found here, compared with previous works from both crab species, suggest that besides the spatial heterogeneity, interspecific competition between parasites could explain the differences observed.

Shade plots, simple visual representations of abundance matrices from multivariate species assemblage studies, are shown to be an effective aid in choosing an overall transformation (or other pre-treatment) of quantitative data for long-term use, striking an appropriate balance between dominant and less abundant taxa in ensuing resemblance-based multivariate analyses. Though the exposition is entirely general and applicable to all community studies, detailed illustrations of the comparative power and interpretative possibilities of shade plots are given in the case of two estuarine assemblage studies in south-western Australia: (a) macrobenthos in the upper Swan Estuary over a two-year period covering a highly significant precipitation event for the Perth area; and (b) a wide-scale spatial study of the nearshore fish fauna from five divergent estuaries. The utility of transformations of intermediate severity is again demonstrated and, with greater novelty, the potential importance seen of further mild transformation of all data after differential down-weighting (dispersion weighting) of spatially ‘clumped’ or ‘schooled’ species. Among the new techniques utilized is a two-way form of the RELATE test, which demonstrates linking of assemblage structure (fish) to continuous environmental variables (water quality), having removed a categorical factor (estuary differences). Re-orderings of sample and species axes in the associated shade plots are seen to provide transparent explanations at the species level for such continuous multivariate patterns.

Macrobenthic data from estuaries along the Pernambuco coast in north-eastern Brazil were analysed to evaluate the effect of sieve mesh size (1.0 mm × 0.5 mm) and sampling depth (0–10 cm × 0–20 cm) on the description of infaunal communities, in an attempt to discuss standardized sampling procedures for different ecological studies objectives in these ecosystems. In general, the difference in sieve retention was less evident for biomass but was important for abundance: the 1.0 mm sieve retained only 27% of total individuals but 77% of total biomass. Regarding sampling depth, the 0–10 cm layer contained most individuals (94%) but contributed just 64% of the overall biomass. Although no strong differences in community structure were observed at most sites with the use of different sieves, the correlations among community dissimilarity using different meshes with environmental parameters (organic matter, total-N and microphytobenthos) indicated that the use of the 0.5 mm sieve will allow a better evaluation of the status of these estuaries. The results also highlight the importance of taking the vertical distribution of tropical macrofauna into account for quantitative estimates: for taxa composition and abundance the top layer is clearly essential, whereas for biomass the deeper layers should also be considered.

A total of 16 species of intertidal brachyuran crabs were recorded from the three major estuaries (Punta Banda, False Bay-San Quintín and Laguna Manuela) of the west coast of the state of Baja California, Mexico. The species belong to 7 families: Cancridae (3), Grapsidae (2), Ocypodidae (2), Panopeidae (3), Pinnotheridae (4), Portunidae (1) and Varunidae (1). New distributional records include an extension of the northern limits of Cyrtoplax schmitti Rathbun, 1935, Panopeus purpureus Lockington, 1877, Goniopsis pulchra (Lockington, 1877), Uca princeps (Smith, 1870) and Pinnixa longipes (Lockington 1877).

The spatial patterns of distribution of five species of the Gerreidae (Diapterus rhombeus, Eucinostomus argenteus, Eucinostomus gula, Eucinostomus melanopterus and Eugerres brasilianus) in Mambucaba estuary, south-eastern Brazil, were determined to assess habitat partitioning of the estuarine reaches. Sampling was conducted between October 2007 and August 2008. Diapterus rhombeus and E. gula were exclusively found in the lower estuary, whereas E. melanopterus and E. brasilianus were exclusively found from the middle estuary. Eucinostomus argenteus was common in the two estuarine zones. Total length and total weight data showed that the smallest individuals of D. rhombeus and E. gula were found near to the estuarine mouth compared with deeper areas of high salinity and lesser influence of the estuarine plume. The smallest individuals of E. argenteus, E. brasilianus and E. melanopterus were found in a protected estuarine lagoon connected to the main estuarine channel, and the largest in the other sites in the main channel of the middle estuary. Spatial partition seems to be the strategy developed by the 5 members of the Gerreidae family to coexist in the Mambucaba estuary, which may be attributed to competition in the past between the species of Gerreidae or to differentiated tolerance to environmental constraints

Hydrobia ulvae displays an endogenous rhythm of crawling behaviour of circatidal periodicity, with higher levels of activity during high water. In the present study we address the effect of repeated cycles of immersion and emersion at tidal periodicity on the level and synchronism of the behaviour, by contrasting these with the effects of continuous immersion and continuous emersion. Snails were recorded in dark conditions under the different immersion regimes for 3 days. The results show that continuously emersed snails displayed very low levels of activity. Average activity levels of continuously immersed snails and of those subjected to tidal cycles of immersion and emersion were similar, had identical periods related to the period of the tidal cycle, and had similar phase relationships to the expected tidal cycle. However, form-estimates for these two categories of snails differed, the snails subjected to cyclic conditions showing a larger amplitude and greater synchronism of activity. Therefore, it is concluded that recurrent cycles of immersion and emersion should contribute to well defined cycles of activity in the intertidal environment, with greater activity levels during high water.

Macrobenthic assemblages were examined in three fish estuarine nurseries and related to environmental variables, as well as fish and macrocrustaceans, in order to assess and compare the potential foraging ground value of these systems. Macrobenthos was sampled in spring 2007 in the Canche, Authie and Somme estuaries (eastern English Channel, France). A total of 17, 28 and 23 macrobenthic taxa, with a clear dominance of amphipods (mainly Bathyporeia sarsi), polychaetes and bivalves, were recorded in the three estuaries respectively. Although predators (fish and macrocrustaceans) were abundant, relatively high densities of macrobenthos were observed: 876.2 ± 389.1, 595.4 ± 197.2 and 854.3 ± 281.2 ind. m-2 in the Canche, Authie and Somme, respectively. No significant difference in species richness, Shannon–Wiener diversity and density (total and dominant groups) of macrobenthos was observed between the three estuaries. Although the analysis of similarity and similarity percentages analyses indicated that macrobenthic assemblage was variable between Authie and Somme, results showed that macrobenthos resource was relatively high and similar in the three estuaries. Taking into account these considerations, the present study indicated a similar relative importance of the Canche, Authie and Somme estuaries as foraging grounds for fish and macrocrustaceans during spring. Multivariate analysis showed that macrobenthic assemblages were mainly driven by salinity and sediment characteristics in the Canche and Authie estuaries while in the Somme estuary sediment characteristics were the most influencing parameters.

We investigated the occurrence and seasonal variation of the biomass of rotifers, tintinnids, the heterotrophic dinoflagellate Gyrodinium fusus and copepod nauplii in the Bahía Blanca Estuary (38°42′S61°50 ′W), Argentina, during an annual cycle. The rotifers fauna comprised three species, while the tintinnids were represented by sixteen species. The biomass of the rotifers fluctuated between 0.62 and 8.90 µgC l−1. The biomass of the tintinnids fluctuated between 0.13 and 9.37 µgC l−1, the biomass of the nauplii stages between 1.78 and 7.65 µgC l−1; while the biomass of G. fusus varied from 0.26 and 7.94 µgC l−1, these results are compared to estimates of microzooplankton in other regions. We analysed the presence of the different groups in relation to the environmental variables, based on point-biserial correlation. Salinity fluctuated between 25.14 and 36.64; temperature between 7.5 and 23.2°C, solar radiation between 0.9 and 30.8 MJ m−2d−1 and Secchi distance between 0.25 and 1.43 m. Rotifers were correlated positively with temperature, chlorophyll-a and Secchi depth and negatively with salinity. The tintinnids were positively correlated with salinity. Gyrodinium fusus was positively correlated with Secchi depth, and chlorophyll-a, and negatively with temperature and solar radiation. Nauplii stages were negatively correlated with chlorophyll-a. Based on the occurrence of the microzooplankters in relation to the physico-chemical variables, it was possible to establish two seasonal assemblages: (a) the co-occurrence of the rotifers and the heterotrophic dinoflagellate G. fusus during the winter–spring; and (b) the tintinnids and nauplii larvae during the summer. We conclude that, in this estuary, physico-chemical variables are the forcing factors that directly, or indirectly, influence the seasonal assemblages of the microzooplankton.