All of the contaminant data (from water samples) used in this report were from the Florida DEP STOrage and RETrieval (STORET) database through June 2017, and data were retrieved from the EPA Water Information Network (WIN) data base from July 2017 to the present. STORET and WIN are computerized environmental data systems containing water quality, biological, and physical data.

Advances in analytical technology during the last 20 years have dramatically reduced the concentration at which some chemicals can be detected. This can skew interpretations of temporal trends, which we attempted to avoid by the following actions. Negative values were removed, and values designated as present below the quantitation limit (QL) were replaced with the average of the method detection limit (MDL) and practical quantitation limit (PQL). For “non-detect” values, half the MDL was used; and, for values designated as “zero” the MDL was used. Data designated with a matrix of “ground water”, “surface water sediment,” “stormwater,” “sediment”, or “unknown” were removed. Records with no analytical procedure listed were also removed. Using MDLs reduces the possibility of erroneously concluding there is an increasing trend because of differences in analytical detection limits.

Data are presented in box and whisker plots, which consist of a five-number summary including: a minimum value; value at the first quartile; the median value; the value at the third quartile; and the maximum value. The size of the box is a measure of the spread of the data with the minimum and maximum values indicated by the whiskers. The median value is the value of the data that splits the data in half and is indicated by the horizontal blue line in the center of the boxes. Data are also presented as yearly mean ± standard deviation and compared to the designated reference values.  Graphs are presented for the entire LSJR (including tributaries), the freshwater and saltwater portions of LSJR mainstem, as well as for the tributaries in some cases.

The data (from sediment samples) used in this report came from WIN (2017-present) and STORET (managed by the EPA and FDEP; SLES 1988), designated with a matrix of  “surface water sediment,” or “sediment”. Data were also obtained from several major studies carried out on the Lower St. Johns River from 1983 to 2007. The studies were conducted by the SJRWMD (Delfino et al. 1992: Delfino et al. 1991; Durell et al. 2004; Higman et al. 2013) and the Florida Department of Environmental Protection (Delfino et al. 1991; Pierce et al. 1988). Data were used from the National Oceanographic and Atmospheric Administration’s National Status and Trends Mussel Watch program (NOAA 2007b) and Benthic Surveillance Watch (NOAA 2007a) program.  Cooksey and Hyland 2007b) and Dames and Moore 1983) also generated data that were analyzed in this report. Data from an extensive set of studies conducted by the SJRWMD, which provided a long-term sediment quality assessment of the LSJR, were also included (Durell et al. 2004; Durell et al. 1997; Higman et al. 2013).

Negative values were removed, and values designated as present below the QL were replaced with the average of the MDL and PQL. For “non-detect” values, half the MDL was used; and, for values designated as “zero” the MDL was used.

In some cases, sediment contamination was assessed by calculating average concentrations, percent exceedances of sediment quality guidelines, and average toxicity quotients, or toxicity pressure. These parameters were compared between years and regions of the river. Trends were assessed by plotting mean and median annual concentrations against time and determining the significance of an upward or downward slope of any line (Spearman Rank correlation coefficients p < 0.05). Because of the limitations of the data, all trends were confirmed by graphical analysis and Pearson Product coefficient > 0.5.

There are numerous sources of variability in reported sediment concentrations, including analytical differences, sampling variations, physical and chemical characteristics of the sediment, and even differences in definitions of reporting parameters such as MDLs. Furthermore, there are large differences in the numbers of samples in different regions, all taken at irregular intervals. These data gaps limit the applicability of many different standard statistical tests. Thus, major harmful contaminants and their spatial and temporal trends can be difficult to positively identify and requires judicious use of statistics and careful review of all data.

Environmental toxicology is the study of the effects of contaminants on ecosystem inhabitants, from individual species to whole communities. While toxicity is often viewed in terms of human health risk, human risk is one of the most difficult toxicity “endpoints,” or measures, to accurately quantify. The effects on ecosystems and aquatic organisms are the focus of our assessment of contaminants in the LSJR although human health effects from mercury in fish are discussed.

The environmental impact of a toxic compound can be evaluated several ways. One way is by comparing the concentrations in the LSJR to various toxicity measures. When the concentration of a contaminant in sediment is greater than the toxicity measure, it is an exceedance. Most sediment quality guidelines for contaminants are based on the impact of contaminants on sediment-dwelling benthic macroinvertebrates, assessing both the individual species’ health and the community structure. Since these organisms are at the beginning of the fisheries food chain, their health is a good indicator of general river health. One toxicity measure that is quite protective of the health of aquatic organisms is a Threshold Effects Level (TEL). This is the concentration at which a contaminant begins to affect some sensitive species. When the number of sites that have concentrations greater than the TEL is high, there is a higher possibility that some sensitive organisms are affected. A second, less protective guideline is the Probable Effects Level (PEL). This is the concentration above which many aquatic species are likely to be affected. The TEL and PEL sediment quality guidelines for marine systems and freshwater systems when available are used in this assessment. The marine guidelines were most widely available for the compounds of interest, plus much of the heavily impacted areas are in the marine section of the LSJR. Some alternative guidelines are used and identified for some compounds for which there were no marine TEL or PEL guidelines (MacDonald 1994; NOAA 2008). Specific values are listed in Appendix 5.1.A.

While sediment quality guidelines are useful tools, it is important to appreciate the limitations of simple comparisons in the extremely complex LSJR. A major difficulty in assessing toxic impacts is that the accessibility, or bioavailability, of a contaminant to organisms may vary with sediment type. Two sediments with similar contaminant concentrations but different physical and chemical features can produce very different environmental impacts, and we know that LSJR sediments are highly variable. Furthermore, each sediment quality guideline can be specific to certain organisms and endpoints (e.g., death of fish, reproductive effects of sea urchin, sea worm community structure, etc.) and cannot easily be extrapolated to other organisms or endpoints. Consequently, guidelines from different organizations are sometimes different. Finally, separate guidelines are often established for marine and freshwater environments, though few estuarine guidelines exist that apply to the LSJR. These challenges limit our assessment of the impacts of various contaminants on the LSJR to one that is general and relative in scope.

The LSJR is impacted from various sources of pollution including stormwater runoff from agricultural areas and from urban and suburban areas, discharge of partially treated wastewater from utilities, and contaminants that enter the SJR from the upper and middle basins.