Shallow Water Sites Research Articles

Mute Swans’ Impact on Submerged Aquatic Vegetation in Chesapeake Bay

Abstract: Mute swans (Cygnus olor) are poorly studied despite their potential to impact submerged aquatic vegetation (SAV). We measured vegetation characteristics (i.e., percent cover, shoot density, and canopy ht) of SAV beds in controls (unfenced), 2‐year exclosures, and 1‐year exclosures at 18 sites in the Chesapeake Bay, Maryland, USA, to quantify the impact of herbivory by mute swans on SAV during 2003 and 2004. Mute swan herbivory had a substantial adverse impact on percent cover, shoot density, and canopy height of SAV. At the end of the study mean percent cover, shoot density, and canopy height in the controls were lower by 79%, 76%, and 40%, respectively, as compared to those in 2‐year exclosures. During 2004, percent cover, shoot density, and canopy height increased by 26%, 15%, and 22%, respectively, between early and late seasons of SAV growth in exclosures, but they decreased by 36%, 41%, and 18%, respectively, in the controls. Paired mute swans predominantly occupied 6 of 7 moderate‐depth sites (0.76‐0.99 m), and these sites experienced less (i.e., 32‐75%) SAV reduction. All (n = 7) shallow water sites (0.50‐0.75 m) were predominantly occupied by mute swan flocks, and percent cover reduction of SAV was as high as 75‐100% at these sites. Mute swan flocks also predominantly occupied 3 of the 5 deep‐water sites (≥1 m) and 1 of 7 moderate‐depth sites, wherein we recorded considerable (i.e., 77‐93%) SAV reduction. Thus, considering that flocks are more detrimental to SAV as compared to paired mute swans, we recommend that initial emphasis primarily be placed on controlling mute swans in flocks and secondarily on pairs.

Distribution, abundance and biology of the smalltooth sandtiger shark Odontaspis ferox (Risso, 1810) (Lamniformes: Odontaspididae)

The smalltooth sandtiger shark, Odontaspis ferox, has a cosmopolitan distribution across warm temperate and tropical waters, and although essentially demersal, it has also been captured pelagically in mid-ocean. The species often occurs inshore at steeply shelving coastal and insular locations, and has now been identified by divers at eight widely separated shallow water sites. In the Southern Hemisphere, most O. ferox were caught by trawl on the continental slope, where its bathic range was extended to at least 880 m. Large specimens (>200 cm TL) were found across the whole depth range, but almost all juveniles were caught between 200 and 600 m. The largest recorded male was 344 cm TL, and female 450 cm TL. The few biological data suggest that size at maturity for males is around 200–250 cm TL, and for females 300–350 cm. No pregnant females were recorded but size at birth is probably about 100 cm TL. Nowhere has the species been found in large numbers. Survey and commercial catch data from south-east Australian trawl grounds suggest that numbers of O. ferox there have declined since the advent of deepwater commercial trawling in the 1970s. In areas of steep untrawlable terrain, increased gill-netting and longlining are likely to impact on local populations, with mature individuals being particularly vulnerable. Although O. ferox is not specifically targeted by commercial fishing activities, its likely very low fecundity make it susceptible to local extirpation, even at seemingly small capture rates. This species is protected off New South Wales and is considered “vulnerable” globally, by the World Conservation Union (IUCN).

Bayesian focalization: Quantifying source localization with environmental uncertainty

This paper applies a Bayesian formulation to study ocean acoustic source localization as a function of uncertainty in environmental properties (water column and seabed) and of data information content [signal-to-noise ratio (SNR) and number of frequencies]. The approach follows that of the optimum uncertain field processor [A. M. Richardson and L. W. Nolte, J. Acoust. Soc. Am. 89, 2280-2284 (1991)], in that localization uncertainty is quantified by joint marginal probability distributions for source range and depth integrated over uncertain environmental properties. The integration is carried out here using Metropolis Gibbs' sampling for environmental parameters and heat-bath Gibbs' sampling for source location to provide efficient sampling over complicated parameter spaces. The approach is applied to acoustic data from a shallow-water site in the Mediterranean Sea where previous geoacoustic studies have been carried out. It is found that reliable localization requires a sufficient combination of prior (environmental) information and data information. For example, sources can be localized reliably for single-frequency data at low SNR (-3 dB) only with small environmental uncertainties, whereas successful localization with large environmental uncertainties requires higher SNR and/or multifrequency data.

Assessment of Tidal Current Resources: Case Studies of Estuarine and Coastal Sites

The potential for tidal stream power in North Western European waters is large and a number of axial flow, vertical rotor and oscillating hydroplane schemes are approaching full scale design and construction. The accurate determination of the available or potential fluid power is being addressed by, in particular, the regulatory bodies as they move towards the establishment of industry standards and the identification and designation of licensing areas. A generic formulation is developed here which utilises Admiralty tidal diamond data and the arithmetic summation of harmonics due to the lunar semi-diurnal, the solar semi-diurnal and (for shallow water and estuarine sites) the lunar quarter diurnal components. Numerical and sensitivity analyses show that the long term potential power is sensitive to the amplitudes of the harmonics but insensitive to the frequencies and phase differences. The results are applied to estuarine sites off Immingham and at Hull Roads in the Humber and to a shallow water, coastal site off Weston-super-Mare in the Bristol Channel. The results indicate that the shore side energy output from a small scale, meso-generation, 100 m2 capture area device with 60% efficiency varies from about 600 MWha−1 in the Bristol Channel to about 900 MWha−1 in the Humber where the ebb dominated tide flows for longer durations and at slightly higher speeds.

Assessment of Tidal Current Resources: Case Studies of Estuarine and Coastal Sites

The potential for tidal stream power in North Western European waters is large and a number of axial flow, vertical rotor and oscillating hydroplane schemes are approaching full scale design and construction. The accurate determination of the available or potential fluid power is being addressed by, in particular, the regulatory bodies as they move towards the establishment of industry standards and the identification and designation of licensing areas. A generic formulation is developed here which utilises Admiralty tidal diamond data and the arithmetic summation of harmonics due to the lunar semi-diurnal, the solar semi-diurnal and (for shallow water and estuarine sites) the lunar quarter diurnal components. Numerical and sensitivity analyses show that the long term potential power is sensitive to the amplitudes of the harmonics but insensitive to the frequencies and phase differences. The results are applied to estuarine sites off Immingham and at Hull Roads in the Humber and to a shallow water, coastal site off Weston-super-Mare in the Bristol Channel. The results indicate that the shore side energy output from a small scale, meso-generation, 100 m2 capture area device with 60% efficiency varies from about 600 MWha–1 in the Bristol Channel to about 900 MWha–1 in the Humber where the ebb dominated tide flows for longer durations and at slightly higher speeds.

Environmental Manipulation to Avoid a Unique Predator: Drinking Hole Excavation in the Agile Wallaby, Macropus agilis

AbstractThe simplest way of avoiding an ambush predator is to entirely avoid the habitat in which it hunts. However, this strategy requires that the prey species find alternative, risk‐free sources of essential resources. Herein we describe a novel strategy used by agile wallabies (Macropus agilis) to avoid saltwater crocodile (Crocodylus porosus) predation: the creation of risk‐free sites to obtain water. We studied the anti‐predator behaviour of agile wallabies for 3 yr during the dry season along the Daly River, Northern Territory, Australia. Wallabies excavated holes in the sand 0.5–18.0 m from the water's edge, and preferred to drink from these holes over drinking from the river. We determined a hierarchy of preferred drinking‐site options for the wallabies: non‐river sites: springs, puddles, excavated holes; and river sites: sites with cover, shallow water sites and deep water sites. Drinking holes were twice as far from the water's edge in a river stretch with high crocodile density (2/km) than those in a stretch with low crocodile density (0.08/km). However, site differences could also be explained by river bank morphology. Collectively, our findings indicate that agile wallabies excavate drinking holes to avoid crocodile predation. We contend that this behaviour represents environmental manipulation specifically to alter the risk associated with obtaining a key resource.

Insights on geochemical cycling of U, Re and Mo from seasonal sampling in Boston Harbor, Massachusetts, USA

This study examined the removal of U, Mo, and Re from seawater by sedimentary processes at a shallow-water site with near-saturation bottom water O 2 levels (240–380 μmol O 2/L), very high organic matter oxidation rates (annually averaged rate is 880 μmol C/cm 2/y), and shallow oxygen penetration depths (4 mm or less throughout the year). Under these conditions, U, Mo, and Re were removed rapidly to asymptotic pore water concentrations of 2.2–3.3 nmol/kg (U), 7–13 nmol/kg (Mo), and 11–14 pmol/kg (Re). The depth order in which the three metals were removed, determined by fitting a diffusion-reaction model to measured profiles, was Re < U < Mo. Model fits also suggest that the Mo profiles clearly showed the presence of a near-interface layer in which Mo was added to pore waters by remineralization of a solid phase. The importance of this solid phase source of pore water Mo increased from January to October as the organic matter oxidation rate increased, bottom water O 2 decreased, and the O 2 penetration depth decreased. Experiments with in situ benthic flux chambers generally showed fluxes of U and Mo into the sediments. However, when the overlying water O 2 concentration in the chambers was allowed to drop to very low levels, Mn and Fe were released to the overlying water along with the simultaneous release of Mo and U. These experiments suggest that remineralization of Mn and/or Fe oxides may be a source of Mo and perhaps U to pore waters, and may complicate the accumulation of U and Mo in bioturbated sediments with high organic matter oxidation rates and shallow O 2 penetration depths. Benthic chamber experiments including the nonreactive solute tracer, Br −, indicated that sediment irrigation was very important to solute exchange at the study site. The enhancement of sediment–seawater exchange due to irrigation was determined for the nonreactive tracer (Br −), TCO 2, NH 4 + , U and Mo. The comparisons between these solutes showed that reactions within and around the burrows were very important for modulating the Mo flux, but less important for U. The effect of these reactions on Mo exchange was highly variable, enhancing Mo (and, to a lesser extent, U) uptake at times of relatively modest irrigation, but inhibiting exchange when irrigation rates were faster. These results reinforce the observation that Mo can be released to and removed from pore waters via sedimentary reactions. The removal rate of U and Mo from seawater by sedimentary reactions was found to agree with the rate of accumulation of authigenic U and Mo in the solid phase. The fluxes of U and Mo determined by in situ benthic flux chamber measurements were the largest that have been measured to date. These results confirm that removal of redox-sensitive metals from continental margin sediments underlying oxic bottom water is important, and suggest that continental margin sediments play a key role in the marine budgets of these metals.

Effects of organic effluents from a salmon farm on a fjord system. II. Temporal and spatial patterns in infauna community composition

This study examined spatial and temporal variations in infaunal community composition in a gradient away from a large salmon farm (producing 2910 tonnes during each production cycle) in Uggdalsfjorden, western Norway. The farm is located at a water depth of 230 m, is moored at a single point and moves with prevailing currents and winds. The study showed that the large-scale effects on the benthos were restricted to the nearest 250 m of the farm. This zone was dominated by the polychaetes Paramphinome jeffreysii, Prionospio steenstrupi, Capitella capitata and Heteromastus filiformis, the bivalves Thyasira sarsii and Abra nitida and the echinoderm Brissopsis lyrifera for the duration of the two-year study. Highest abundance and biomass were recorded at peak production at the farm, with 30 000 individuals m − 2 and 60 g ash-free dry weight (AFDW) m − 2 . At this time abundance was 10 and biomass was 35 times higher within 250 m from the farm than 3 km away. Highest species richness was found 550–900 m from the farm, where, at peak production, the number of species doubled from 20 to 40 species per 0.1 m − 2 . The study showed that at deep sites organic waste affects benthos on a spatial scale much larger than at shallow water sites, and although the infauna community composition varied over time, the consistency in the spatial pattern in the relationship between species richness, abundance and biomass in the course of the study indicates that the observed patterns were temporally stable. The loadings of organic matter from the farm did not exceed the capacity of the benthic community for decomposition, as indicated by the low and stable content of organic matter in the sediment around the farm.

Micro-habitats of brackish water ostracods from Poel Island, southern Baltic Sea coast

Five different micro-habitats were checked for ostracod distribution in a brackish shallow water site in the mesohaline salinity range. Ostracods were counted semi-quantitatively and their speed of movement and behaviour were observed. The micro-habitats are sandy and muddy sediment (epifaunal and shallow infaunal) as well as filamentous green algae,Fucus vesiculosus (macro-algae) andMytilus edulis (mussel) colonies. Within the nine documented ostracod species are five species dominating the different micro-habitats:Leptocythere psammophila andCyprideis torosa clearly dominate the sediment (L. psammophila shallow infaunal andC. torosa infaunal to epifaunal). In most sediment samples,Loxoconcha elliptica was found in small numbers, but it is frequent on all other substrates, especially the mussel colonies.Xestole-beris nitida is typical for mussel colonies andSemicytherura nigrescens for macro-algae.

Matched-field geoacoustic inversion with a horizontal array and low-level source

This paper applies geoacoustic inversion to acoustic-field data collected on a bottom-moored horizontal line array due to a continuous-wave towed source at a shallow water site in the Barents Sea. The source transmitted tones in the frequency band of 30–160Hz at levels comparable to those of a merchant ship, with resulting signal-to-noise ratios of 9–15dB. Bayesian inversion is applied to cross-spectral density matrices formed by averaging spectra from a sequence of time-series segments (snapshots). Quantifying data errors, including measurement and theory errors, is an important component of Bayesian inversion. To date, data error estimation for snapshot-averaged data has assumed either that averaging reduces errors as if they were fully independent between snapshots, or that averaging does not reduce errors at all. This paper quantifies data errors assuming that averaging reduces measurement error (dominated by ambient noise) but does not reduce theory (modeling) error, providing a physically reasonable intermediary between the two assumptions. Inversion results in the form of marginal posterior probability distributions are compared for the different approaches to data error estimation, and for data collected at several source ranges and bearings. Geoacoustic parameter estimates are compared with data from supporting geophysical measurements and historical data from the region.

Analysis of DGGE profiles to explore the relationship between prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin

The aim of this work was to relate depth profiles of prokaryotic community composition with geochemical processes in the deep subseafloor biosphere at two shallow-water sites on the Peru Margin in the Pacific Ocean (ODP Leg 201, sites 1228 and 1229). Principal component analysis of denaturing gradient gel electrophoresis banding patterns of deep-sediment Bacteria, Archaea, Euryarchaeota and the novel candidate division JS1, followed by multiple regression, showed strong relationships with prokaryotic activity and geochemistry (R(2)=55-100%). Further correlation analysis, at one site, between the principal components from the community composition profiles for Bacteria and 12 other variables quantitatively confirmed their relationship with activity and geochemistry, which had previously only been implied. Comparison with previously published cell counts enumerated by fluorescent in situ hybridization with rRNA-targeted probes confirmed that these denaturing gradient gel electrophoresis profiles described an active prokaryotic community.

Vertical directionality of noise at two shallow water sites

Noise recorded with 16-element vertical line arrays moored at two sites near 80-m water depth has been analyzed. One site is south of New England (Shelfbreak PRIMER, June 1996), the other south of China in the South China Sea (ASIAEX, May 2001). Both sites exhibited downward refracting conditions, so that a noise notch is realizable, and both exhibit internal gravity waves. The waves were more plentiful and of larger amplitude at the South China Sea site. Sound in a 40-Hz band centered at 135 Hz was extracted and separated into vertical beams using delay and sum beamforming. At each location, noise lower than the median level exhibited a peak near zero degrees for each data set (near-horizontal arrival). Noise higher than the median level in the New England data set exhibited a 5-dB noise notch, with peak levels at about ±15 deg. Noise higher than the median level in the South China Sea data set did not show the notch and was essentially flat between 10 and −10 deg. The results are consistent with observed fluctuating propagation between fixed sources and re- ceivers at the sites, and with differences in coupled-mode propagation through the two internal-wave fields.

Estimating mutual information for the underwater acoustic channel

Estimates of the upper and lower bounds on the information rates attainable for acoustic communication systems with white Gaussian sources under uncertain channel conditions are provided that account for finite duration signaling and finite coherence time. For the case where the coherence time of the channel exceeds that of the packet duration the estimators are computationally efficient with the Levinson recursion and provide a means of tuning the accuracy of the estimates to fit a given computational budget. The reduction in the information rate relative to the known channel case is quantified in terms associated with the duration of signaling, the posterior covariance of the channel, and the prior covariance of the channel. For scenarios where the prior channel covariance is known exact bounds on the information rates are computable else the estimators provide confidence intervals for these rates. The estimators are tested on 18 kHz at sea data collected in shallow water north of Elba Italy on a 1.8-m aperture vertical array and on very shallow water sites at Keyport Washington. The effects of temporal coherence degradation as well as multi-path spread are quantified. [Work supported by the Office of Naval Research.]

Acoustic backscatter measurements from littoral seabeds at shallow grazing angles at 4 and 8 kHz

Direct measurement of acoustic scattering from the seabed at shallow grazing angles and low kilohertz frequencies presents a considerable challenge in littoral waters. Specifically, returns from the air-water interface typically contaminate the signals of interest. To address this issue, DRDC Atlantic has developed a sea-going research system for measuring acoustic scatter from the seabed in shallow-water environs. The system, known as the wideband sonar (WBS), consists of a parametric array transmitter and a superdirective receiver. In this paper, backscatter measurements obtained with the WBS at two sandy, shallow-water sites off North America's Atlantic coast are presented. Data were collected at 4 and 8 kHz at grazing angles from 3 degrees-15 degrees. The backscattering strength is similar at both sites and, below about 8 degrees, it appears to be independent of frequency within the statistical accuracy of the data. The measurements show reasonable agreement with model estimates of backscatter from sandy sediments. A small data set was collected at one of the sites to examine the feasibility of using the WBS to measure the azimuthal variability of acoustic scatter. The data set--although limited--indicates that the parametric array's narrow beamwidth makes the system well-suited to this task.

Demography and reproductive ecology of the Columbia spotted frog (Rana luteiventris) across the Palouse

Here we report on the demography and reproductive ecology of the Columbia spotted frog (Rana luteiventris Thompson, 1913) breeding in ponds across the Palouse Bioregion of Washington and Idaho. Spotted frogs are unusual, if not unique, among temperate ranids in that males establish the oviposition site before females become active. Females laid at one or two communal sites in shallow water. Our breeding populations were small, never exceeding 50 adults counted, and most displayed male-biased sex ratios. We estimated effective population sizes (Ne) as ranges determined by extremes in male breeding success; these varied between 3.2 and 37.8. Even the latter falls below the minimum required for long-term population viability. Small population size may make spotted frogs vulnerable to genetic problems and environmental insults. Communal oviposition certainly renders a population's reproductive effort vulnerable to variation in hydroperiod, which we observed during the dry spring of 2004. In the absence of information on the degree of "connectedness" among our ponds as subunits of more resilient metapopulations, we suggest that small population size and communal oviposition likely render R. luteiventris vulnerable to anthropogenic disturbance. Furthermore, the status of R. luteiventris on the Palouse may be less secure than assumed currently.

Infection characteristics of a trematode in an estuarine isopod: influence of substratum

The estuarine isopod Cyathura carinata is a second intermediate host to microphallid trematodes, which use mud snails Hydrobia spp. and shorebirds as respectively first intermediate and final hosts. To identify processes responsible for infection patterns observed in C. carinata, a short-term microcosm experiment was conducted with both macroinvertebrates and one of their common parasites – Maritrema subdolum. Fine sand collected from two different shallow water sites was used to test if sediment type could affect infection rates. After 7 days at 25 °C, C. carinata from the substratum with the highest proportion of particles <125 μm were more surface active and obtained significantly more M. subdolum individuals than isopods from the other sediment type. No parasite-induced effects on the hosts were found during this short-term experiment. The distribution pattern of microphallid cysts and mesocercariae inside the isopods revealed that M. subdolum cercariae primarily penetrated through the pleopods and afterwards located themselves in the middle-posterior region of the host’s body. Even if it was not possible to identify the factor responsible for the observed infection patterns (cercariae production and/or host behaviour), the results of this experiment indicate that small-scale factors, such as differences in substratum and associated features, may have considerable impact on infections of host populations.

The nature of the δ 13C of periplatform sediments: Implications for stratigraphy and the global carbon cycle

The carbon-isotopic composition (δ 13C) of bulk carbonates, obtained from a transect of sites drilled through platform and periplatform sediments of Holocene to Early Miocene age, has been compared to ascertain whether changes in the δ 13C can be correlated between sediments of equivalent ages and whether such changes can be related to global changes in the δ 13C of the dissolved inorganic carbon in the oceans over this time period. Five of the sites were drilled during Leg 166 of the Ocean Drilling Project (1003–1007) in a transect ranging from five km to 25 km away from the platform margin and penetrating sediments of Holocene to Oligocene age that are contained in 17 depositional sequences (A–Q). Two shallow-water sites, Clino and Unda were situated on a extension of the same transect on Great Bahama Bank in a water depth of 10–15 m. With the exception of Unda and Clino, the δ 13C of the carbonates ranges from +5‰ in the younger sequences to +1‰ in the Early Miocene. In each of the sites, the δ 13C is strongly positively correlated with the percentage of aragonite. As a consequence, the δ 13C of sequences A through F is strongly correlated, reflecting the decreasing amount of aragonite with increasing depth. In the two platform sites, the δ 13C is significantly lower in the younger portions of the cores as a result of the influences of meteoric diagenesis during repeated exposure during the Pleistocene. Although the δ 13C of the individual sequences can be correlated in most instances between the ODP holes, the changes are not related to global changes in the δ 13C of the oceans which in contrast to the δ 13C of the platform sediments become isotopically lower towards the present day. Instead variations in the δ 13C appear to be related to varying mixtures of δ 13C-rich banktop sediments and pelagic material.

Inversion of sonobuoy data from shallow-water sites with simulated annealing

An enhanced simulated annealing algorithm is used to invert sparsely sampled seismic data collected with sonobuoys to obtain seafloor geoacoustic properties at two littoral marine environments as well as for a synthetic data set. Inversion of field data from a 750-m water-depth site using a water-gun sound source found a good solution which included a pronounced subbottom reflector after 6483 iterations over seven variables. Field data from a 250-m water-depth site using an air-gun source required 35,421 iterations for a good inversion solution because 30 variables had to be solved for, including the shot-to-receiver offsets. The sonobuoy derived compressional wave velocity-depth (Vp-Z) models compare favorably with Vp-Z models derived from nearby, high-quality, multichannel seismic data. There are, however, substantial differences between seafloor reflection coefficients calculated from field models and seafloor reflection coefficients based on commonly used Vp regression curves (gradients). Reflection loss is higher at one field site and lower at the other than predicted from commonly used Vp gradients for terrigenous sediments. In addition, there are strong effects on reflection loss due to the subseafloor interfaces that are also not predicted by Vp gradients.

Genetic population structure in the black-spot sea bream (Pagellus bogaraveo Br�nnich, 1768) from the NE Atlantic

The depletion of shallow-water fish stocks through overexploitation has led to increasing fishing pressure on deep-sea species. Poor knowledge of the biology of commercially valuable deep-water fish has led to the serial depletion of stocks of several species across the world. Data regarding the genetic structure of deep-sea fish populations is important in determining the impact of overfishing on the overall genetic variability of species and can be used to estimate the likelihood of recolonisation of damaged populations through immigration of individuals from distant localities. Here the genetic structure of the commercially fished deep-water species the blackspot sea bream, Pagellus bogaraveo is investigated in the northeastern Atlantic using partial DNA sequencing of mitochondrial cytochrome b (cyt-b) and D-loop regions and genotyping of microsatellite loci. An absence of variation in cyt-b and low genetic variation in D-loop sequences potentially indicate that P. bogaraveo may have undergone a severe bottleneck in the past. Similar bottlenecks have been detected in other Atlantic species of fish and have possibly originated from the last glaciation. P. bogaraveo may have been particularly vulnerable to the effects of low temperature and a fall in sea level because stages of its life history occur in shallow water and coastal sites. However, there are other explanations of low genetic variability in populations of P. bogaraveo, such as a low population size and the impacts of fishing on population structure. Analysis of population structure using both D-loop and microsatellite analysis indicates low to moderate, but significant, genetic differentiation between populations at a regional level. This study supports studies on other deep-sea fish species that indicate that hydrographic or topographic barriers prevent dispersal of adults and/or larvae between populations at regional and oceanographic scales. The implications for the management and conservation of deep-sea fish populations are discussed.

Nekton habitat quality at shallow water sites in two Rhode Island coastal systems

We evaluated nekton habitat quality at 5 shallow-water sites in 2 Rhode Island systems by comparing nekton densities and biomass, number of species, prey availability and feeding, and abundance of winter flounderPseudopleuronectes americanus. Nekton density and biomass were compared with a 1.75-m2 drop ring at 3 sites (marsh, intertidal, and subtidal) in Coggeshall Cove in Narragansett Bay and two subtidal sites (eelgrass and macroalgae) in Ninigret Pond, a coastal lagoon. We collected benthic core samples and examined nekton stomach contents in Coggeshall Cove. We identified 16 species of fish, 16 species of crabs, and 3 species of shrimp in our drop ring samples. A multivariate analysis of variance indicated differences in total nekton, invertebrates, fish, and winter flounder across the five sites. Relative abundance of benthic invertebrate taxa did not match relative abundance of prey taxa identified in the stomachs. Nonmetric multidimensional scaling plots showed groupings in nekton and benthic invertebrate prey assemblages among subtidal, intertidal, and marsh sites in Coggeshall Cove. Stepwise multiple regression indicated that biomass of macroalgae was the most important variable predicting abundance of nekton in Coggeshall Cove, followed by elevation and depth. In Rhode Island systems that do not experience chronic hypoxia, macroalgae adds structure to unvegetated areas and provides refuge for small nekton. All sites sampled were characterized by high abundance and diversity of nekton pointing to the importance of shallow inshore areas for production of fishes and decapods. Measurements of habitat quality should include assessment of the functional significance of a habitat (this can be done by comparing nekton numbers and biomass), some measure of habitat diversity, and a consideration of how habitat quality varies in time and space.