Seagrass beds serve critical functions in coastal Florida ecosystems. The beds serve as nursery habitat for many juvenile reef fish species and provide protection for many types of benthic organisms found in Biscayne Bay. They help stabilize sediment that would otherwise increase turbidity around coral reefs, filter the water of contaminants, and help support an entire food web. Three species of seagrass were found at the study sites in northern Biscayne Bay: Thalassia testudinum, Halodule wrightii, and Syringodium filiforme. This study focused on understanding the organism habitat interaction by determining the species diversity, seasonal densities, and the correlation between population size and individual size for Penaeid shrimp, juvenile fish, and small adult fish at each site over a one year period. Habitat selectivity of various species was determined based on the habitat complexity derived from the various different seagrasses found in each of the beds. Animals predominantly favored H. wrightii habitat (Kruskal-Wallis H test: p< 0.0001) and this was likely the result of a decrease in predation risk due to the increased habitat complexity of the seagrass beds. Species diversity did not vary significantly over the course of a year (p= 0.7790), likely due to the lack of large abiotic disturbances (e.g. boating, hurricanes, and extreme salinity changes) to the seagrass beds. Densities of inhabitants changed significantly on a monthly basis, with the overall epifauna densities greatest at the end of the wet season (p< 0.01). The lack of correlation between individual size and overall population size likely indicated the majority of the species caught did not exhibit ontogenetic migration or live in the seagrass beds for the entirety of their life cycle.

In southeastern Florida, the majority of drinking water comes from the Biscayne aquifer. This aquifer is comprised of heterogeneous limestones, sandstones, sand, shell and clayey sand with zones of very high permeability. Visualizing the spatial variations in lithology, porosity and permeability of heterogeneous aquifers, like the Biscayne, can be difficult using traditional methods of investigation. Using the Roxar IRAP RMS software multi-layered 3D conceptual geomodels of the lithology, cyclostratigraphy and porosity were created in a portion of the Biscayne aquifer. The models were built using published data from borehole geophysical measurements, core samples, and thin sections. Spatial relations between lithology, cyclostratigraphy, porosity, and preferential flow zones were compared and contrasted to better understand how these geologic features were inter-related. The models show local areas of differing porosity within and cross-cutting different cycles and lithologies. Porosity in the Biscayne aquifer study area follows a hierarchy attributed to lithofacies with a pattern of increasing porosity for the high frequency cycles. This modeling improves understanding of the distribution and interconnectedness of preferential flow zones, and is thus an invaluable tool for future studies of groundwater flow and groundwater contamination in the Biscayne aquifer. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection

The karst Biscayne aquifer is characterized by a heterogeneous spatial arrangement of porosity, making hydrogeological characterization difficult. In this dissertation, I investigate the use of ground penetrating radar (GPR), for understanding the spatial distribution of porosity variability in the Miami Limestone presented as a compilation of studies where scale of measurement is progressively increased to account for varying dimensions of dissolution features. In Chapter 2, GPR in zero offset acquisition mode is used to investigate the 2-D distribution of porosity and dielectric permittivity in a block of Miami Limestone at the laboratory scale (< 1.0 m). Petrophysical models based on fully saturated and unsaturated. water conditions are used to estimate porosity and solid dielectric permittivity of the limestone. Results show a good correspondence between analytical and GPR-based porosity estimates and show variability between 22.0-66.0 %. In Chapter 3, GPR in common offset and common midpoint acquisition mode are used to estimate bulk porosity of the unsaturated Miami Limestone at the field scale (10.0-100.0 m). Estimates of porosity are based on the assumption that the directly measured water table reflector is flat and that any deviation is attributed to changes in velocity due to porosity variability. Results show sharp changes in porosity ranging between 33.2-60.9 % attributed to dissolution areas. In Chapter 4, GPR in common offset mode is used to characterize porosity variability in the saturated Biscayne aquifer at 100-1000 m field scales. The presence of numerous diffraction hyperbolae are used to estimate electromagnetic wave velocity and asses both horizontal and vertical changes in porosity after application of a petrophysical model. Results show porosity variability between 23.0-41.0 % and confirm the presence of isolated areas that could serve as enhanced infiltration or recharge. This research allows for the identification and delineation areas of macroporosity areas at 0.01 m lateral resolution and shows variability of porosity at different scales, reaching 37.0 % within 1.3 m, associated with areas of enhanced dissolution. Such improved resolution of porosity estimates can benefit water management efforts and transport modelling and help to better understand small scale relationships between ground water and surface water interactions. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection

Accurate hydraulic conductivity values are necessary for understanding groundwater flow. Methods for estimating hydraulic conductivity show limitations because measured values vary several orders of magnitude in high permeability aquifers. Slug tests, while cost and time efficient, result in values lower than expected. It is proposed that underdamped behavior of water in a well is similar to mass on a damped spring; hence, models constructed to simulate behavior independent of aquifer effects might replicate some tests. The Poiseuille and Darcy-Weisbach models, and extensions of these models considering entry/exit effects, are applied to an aquifer-free laboratory test, and real wells. Aquifer-free laboratory tests are modeled well using both Poiseuille and Darcy-Weisbach models with entry/exit effects. The Poiseuille model for wells does not agree with observed data, possibly because of high Reynolds numbers. The Darcy-Weisbach model does agree with well data significantly better, although the friction factor relies on a single Reynolds number.

Inshore tropical and subtropical estuaries harbor a relatively high abundance and diversity of organisms. Specifically within estuaries, mangrove and seagrass habitats provide shelter and food for a plethora of organisms, through some or all their life histories. Given the biological connection between offshore coral reefs and coastal estuaries, there is a critical need to understand the underlying processes that determine distribution and abundance patterns within mangrove-seagrass habitats. The predatory fish assemblage within the mangrove and seagrass beds of Biscayne Bay, Florida (USA), was examined over 24-hr. time periods along a distance and habitat gradient from the mangrove edge and nearshore environment (0–300 m) to farshore (301–700 m) seagrass beds. This thesis also investigated the occurrence, distribution and timing of reef fish movement between offshore coral reef habitat and inshore seagrass beds over 24-hr periods. Results indicate that fish predators differed over both the sampling period and with distance from mangrove edge. The results also demonstrated reef fishes move into Biscayne Bay at dusk and exit at dawn by utilizing Broad Creek Channel as a passageway. This work supports the idea of diel migration of selected reef fishes to inshore seagrass beds and highlights the importance of connective channels between habitats. The results suggest that the degradation or loss of seagrass habitat could differentially impact the life-history stages of reef fish species.

An ecological risk assessment was conducted on the risk to fish of chemical contaminants detected in the habitat of Albula vulpes in South Florida, to evaluate whether contaminants may be a driver of declines in the recreational bonefish fishery. All available contaminant detection data from Biscayne Bay, Florida Bay, and the Florida Keys were compared to federal and state guidelines for aquatic health to identify Contaminants of Potential Ecological Concern (COPECS). For these COPECs, species sensitivity distributions were constructed and compared with recent detections at the 90th centile of exposure. Copper in Biscayne Bay was identified as the highest risk of acute and chronic effects to fish, followed by a risk of chronic effects from both the recently phased-out pesticide endosulfan in Florida Bay, and the pharmaceutical hormone estrone in the Florida Keys.

The anisotropy of the Biscayne Aquifer which serves as the source of potable water for Miami-Dade County was investigated by applying geophysical methods. Electrical resistivity imaging, self potential and ground penetration radar techniques were employed in both regional and site specific studies. In the regional study, electrical anisotropy and resistivity variation with depth were investigated with azimuthal square array measurements at 13 sites. The observed coefficient of electrical anisotropy ranged from 1.01 to 1.36. The general direction of measured anisotropy is uniform for most sites and trends W-E or SE-NW irrespective of depth. Measured electrical properties were used to estimate anisotropic component of the secondary porosity and hydraulic anisotropy which ranged from 1 to 11% and 1.18 to 2.83 respectively. 1-D sounding analysis was used to models the variation of formation resistivity with depth. Resistivities decreased from NW (close to the margins of the everglades) to SE on the shores of Biscayne Bay. Porosity calculated from Archie's law, ranged from 18 to 61% with higher values found along the ridge. Higher anisotropy, porosities and hydraulic conductivities were on the Atlantic Coastal Ridge and lower values at low lying areas west of the ridge. The cause of higher anisotropy and porosity is attributed to higher dissolution rates of the oolitic facies of the Miami Formation composing the ridge. The direction of minimum resistivity from this study is similar to the predevelopment groundwater flow direction indicated in published modeling studies. Detailed investigations were carried out to evaluate higher anisotropy at West Perrine Park located on the ridge and Snapper Creek Municipal well field where the anisotropy trend changes with depth. The higher anisotropy is attributed to the presence of solution cavities oriented in the E-SE direction on the ridge. Similarly, the change in hydraulic anisotropy at the well field might be related to solution cavities, the surface canal and groundwater extraction wells.

The Biscayne Aquifer is a primary source of water supply in Southeast Florida. As a coastal aquifer, it is threatened by saltwater intrusion (SWI) when the natural groundwater flow is altered by over-pumping of groundwater. SWI is detrimental to the quality of fresh groundwater sources, making the water unfit for drinking due to mixing and reactions with aquifer minerals. Increasing water demand and complex environmental issues thus force water utilities in South Florida to sustainably manage saltwater intrusion and develop alternative water supplies (e.g., aquifer storage and recovery, ASR). The objectives of this study were to develop and use calibrated geochemical models to estimate water quality changes during saline intrusion and during ASR in south Florida. A batch-reaction model of saltwater intrusion was developed and important geochemical reactions were inferred. Additionally, a reactive transport model was developed to assess fate and transport of major ions and trace metals (Fe, As) at the Kissimmee River ASR. Finally, a cost-effective management of saltwater intrusion that involves using abstraction and recharge wells was implemented and optimized for the case of the Biscayne Aquifer. Major processes in the SWI areas were found to be mixing and dissolution-precipitation reactions with calcite and dolomite. Most of the major ions (Cl, Na, K, Mg, SO4) behaved conservatively during ASR while Ca and alkalinity were affected by carbonate reactions and cation exchange. A complex set of reactions involving thermodynamic equilibrium, kinetics and surface complexation reactions was required in the ASR model to simulate observed concentrations of Fe and As. The saltwater management model aimed at finding optimal locations and flow rates for abstraction and recharge wells. Optimal solutions (i.e., minimum total salt and total cost Pareto front) were produced for the Biscayne Aquifer for scenarios of surface recharge induced by climate change-affected precipitation. In general, abstraction at the maximum rate near the coast and artificial recharge at locations much further inland were found to be optimal. Knowledge developed herein directly supports the understanding of SWI caused by anthropogenic stressors, such as over-pumping and sea level rise, on coastal aquifers.