Fish and Macroinvertebrate Monitoring in the Lower St. John’s River Basin in Support of the Jacksonville Harbor Deepening Project

By Russell Brodie and Tim MacDonald

The U.S. Army Corps of Engineers (USACE) in cooperation with the Jacksonville Port Authority (JaxPort) have conducted a comprehensive economic, engineering and environmental study to examine the effects of increasing the depth of the existing Federally-maintained shipping channel in the lower St. Johns River (LSJR) from the current depth of 40-feet to a maximum depth of 47-feet between the mouth (Mayport, Florida) and river mile 13 (Figure 1). The channel deepening will allow access of larger vessels (Panamax and New Panamax classes) to deliver cargo to existing JaxPort terminals around Blount Island. The initial phase of dredging began in February 2018.

Figure 1. Map of lower St. Johns River (LSJR) highlighting the area being dredged (river mile 0-13; orange line) and the select tidal tributaries (Trout, Arlington, and Ortega rivers) and the Mill Cove area included in this project funded by the USACE (purple shading). River miles (small circles) represent 1-mile increments along the marked channel. Red lines indicate existing bridges. Base map with river miles and inset created by the SJRWMD and adapted by the FWC FIM program to highlight the current project.

As part of the project evaluation, computer modeling scenarios were completed on the potential effects that the channel deepening might have on water quality, circulation patterns, salinity gradients, and a variety of ecological components (wetland vegetation, submerged aquatic vegetation, benthos, plankton, and nekton [macroinvertebrates and fish]) in the LSJR. Over 100 nekton species have been documented by the Fisheries-Independent Monitoring (FIM) program at the Florida Fish and Wildlife Conservation Commission’s (FWC) Fish and Wildlife Research Institute (FWRI) as using the estuarine portion of the LSJR and many of the species represent important commercial and recreational fisheries. During the evaluation, there were two specific areas the FIM program felt were in need of consideration with respect to nekton: 1) the potential effects of salinity changes on the spawning success, recruitment, and population dynamics of important recreational, commercial, and forage nekton and, 2) the potential effects of salinity changes on critical nekton habitat within the LSJR estuary.

Within the estuary, channel deepening has the potential to affect salinity and water quality gradients, most likely by shifting distributions in these gradients within the estuary. These shifts may affect spawning and nursery habitats and ultimately influence the reproductive and recruitment success of estuarine-dependent nekton. Of particular concern are the tidal tributaries in the LSJR near and upriver from the area being dredged. These tributaries between river miles 15 and 30 (Trout, Arlington, and Ortega rivers; Figure 1) and the estuarine section between Julington Creek (river mile 40) and Palatka (river mile 82; Figure 2) are highly influenced by freshwater inflow and generally have lower salinities than other portions of the LSJR estuary. The freshwater influence in these sections of the LSJR provides low salinity habitats that many estuarine and marine nekton require during their early life history stages. Previously collected data in these tributaries suggests that many recreationally and commercially important estuarine-dependent species (i.e. members of the Sciaenidae family [i.e. red drum, spotted seatrout, atlantic croaker, spot], white shrimp, blue crab, and mullet) utilize these habitats and that these areas likely represent critical habitats for maintaining healthy stocks of these species in the LSJR estuary and adjacent coastal waters. Also of concern with regards to potential changes in salinity would be impacts on resident freshwater species, especially within the Trout, Arlington, and Ortega rivers. Salinity increases could decrease the availability of freshwater habitat, thereby reducing the abundance of freshwater species in these tidal tributaries. The Mill Cove area, although freshwater inflow is limited, is also of concern because the salinity modeling done by the Corps identified it as the area most likely to experience the greatest salinity changes. Young-of-the-year (YOY) and juveniles from numerous nekton species utilize this habitat during ingress, egress, and as nursery habitats.

Figure 2. Map of lower St. Johns River (LSJR) highlighting the long-term sampling area between Julington Creek (river mile 40) and Palatka (river mile 82; purple shading) previously funded by the SJRWMD and now funded by this USACE project. River miles (small circles) represent 1-mile increments along the marked channel. Red lines indicate existing bridges. Base map with river miles and inset created by the SJRWMD and adapted by the FWC FIM program to highlight the current project.

Since 2001, the Fisheries-Independent Monitoring (FIM) program has monitored nekton abundance and distribution in the LSJR estuary downstream of Julington Creek (river mile 40; Figure 1). Between 2005 and 2016, funding from the St. Johns River Water Management District (SJRWMD) enabled the FIM program to extend sampling upriver from Julington Creek (river mile 40) to Palatka (river mile 82; Figure 2). The FIM program uses a multi-gear approach in a stratified-random sampling design to collect data on nekton from a wide range of habitats and life history stages. Water chemistry, habitat, and physical parameters are recorded at each sampling site. The FIM program sampling was designed to monitor fishery resources in the estuary as a whole and, therefore, does not include individual tributaries as specific sampling strata, but instead includes them as portions of larger geographic strata. The spatial extent of the tributaries is very small compared to that of the entire estuary, so the individual tributaries are often underrepresented and inconsistently sampled in the current sampling design. Data from the existing FIM program design, therefore, are not sufficient to assess changes in nekton composition and abundance due to perturbations, such as a channel deepening, within specific areas (tidal tributaries and coves). Estimating impacts to the nekton assemblage from the channel deepening in these areas requires a sampling strategy that focuses on these specific areas of the LSJR estuary.

To gain a better understanding of the relationships between channel deepening, salinity, water quality, water flow, estuarine habitats, and the abundance of estuarine-dependent and freshwater-resident species that inhabit the identified areas of the LSJR, the FIM program and the USACE have developed a long-term monitoring project to determine the impact of the dredging activities on the spatial distribution and abundance of nekton within the LSJR. The long-term monthly sampling, which began in May 2017, and has the potential to run through 2035 (funding dependent), will increase the resolution of nekton data within the identified tidal tributaries (Trout, Arlington, and Ortega rivers) and the Mill Cove area (Figure 1) as well as continue the long-term sampling upstream of Julington Creek (Figure 2), for which funding from the SJRWMD was withdrawn at the end of 2016. This project will allow for the assessment of the effects of channel deepening on nekton assemblages in these critical LSJR estuarine habitats.