Water quality parameters vary as a function of time or tide, others vary by depth, and still others change slowly with the seasons or do not have a consistent pattern of change. Despite these variations, similarities exist within segments of the mainstem of the LSJRB as well as among and within each tributary.

To identify characteristically similar segments in each separate water body, a unique water body identifier (WBID) number is assigned to each water body in the State. WBIDs offer an unambiguous method of referencing waterbodies within the State of Florida. The mainstem of the LSJRB is divided into multiple segments, WBIDs 2213A through 2213N, that range from marine to freshwater systems. The section we refer to as marine/estuarine in this report spans from the mouth at WBID 2213A to WBID 2213H, which contains Doctors Lake. The freshwater region extends from WBID 2213I upstream to WBID 2213N at the confluence of the Ocklawaha River (Figure 2.1).

The Clean Water Act mandates that each water body, each WBID, must be assessed for impairments for its stated uses. The LSJR is a Florida Class III water body with designated uses of recreation, propagation and maintenance of a healthy, well-balanced population of fish and wildlife. If a water body is determined to be impaired for its designated uses, a Total Maximum Daily Load (TMDL) must be established to set maximum allowable levels of pollutants that can be discharged into it that will allow it to achieve water quality standards.

In certain cases, the type and character of a water body may make it necessary to establish a special criterion for assessing the water quality of that water body. Florida’s water quality standards also provide that a Site-Specific Alternative Criterion (SSAC) may be established, where that alternative criterion is demonstrated, based on scientific methods, to protect existing and designated uses for a particular water body. As discussed in the background section and below, such criteria have been established and approved for dissolved oxygen (DO) in the predominantly marine portion of the LSJRB and during certain times of the year when sensitive species may be present.

The water quality of each segment of a river or tributary is strongly impacted by the land use surrounding the water body. Thus, the segments and tributaries of the LSJR vary in water quality impacts from agricultural, industrial, urban, suburban, and rural land uses. Often, different parts of the same stream will have changes in water quality that reflect changes in land use, industry, and population along it. Identification of sources of nutrients or pollutants in the watershed of an impaired water body is part of the TMDL process and the amount of pollutants discharged by each of these sources must be quantified.

Sources of pollutants are broadly classified as either “point sources” or “nonpoint sources.” Historically, point sources are defined as discharges that typically have a continuous flow via a specific source, such as a pipe. Domestic and industrial wastewater treatment facilities (WWTFs) are examples of point sources. Point sources are registered and permitted under the EPA’s National Pollutant Discharge Elimination System (NPDES) program. Changes to the Clean Water Act made in 1987 included a redefinition that added storm water and drainage systems, which were previously considered nonpoint sources under the permitted NPDES program. The term “nonpoint sources” has been used to describe other intermittent, often rainfall-driven, diffuse sources of pollution, including runoff from urban land uses, runoff from agriculture, runoff from tree farming (silviculture), runoff from roads and suburban yards, discharges from failing septic systems, and even atmospheric dust and rain deposition. The Florida Legislature created the Surface Water Improvement and Management program (SWIM) to manage and address nonpoint pollution sources. The program is outlined in DEP 2008c.

The required TMDL process for impaired waters considers and can require reductions to both these pollution source types in order to achieve water quality goals. For more about Florida’s Watershed Management approach, see DEP 2010h. In addition, a description of the Basin Management Action Plan (BMAP), which details actions to be taken in a specific basin, can be found at DEP 2010b. The status of Northeast District BMAP plans can be found at DEP 2013e.

The LSJRB mainstem BMAP was completed in 2008 (DEP 2008a), and a five-year progress report on meeting the TMDL for nutrients was recently released in 2014 (DEP 2014a). There have been two BMAPs completed for a total of 25 tributaries in the lower basin (DEP 2009b; DEP 2010a) and Phase 2 updates completed in 2016 (DEP 2016e; DEP 2016c).