When emaciated Florida manatees started washing up dead in the Indian River Lagoon, the Tampa Bay Times wanted to understand why.

Investigative reporter Zachary T. Sampson chronicled the crisis while covering the environment in 2021, but it was clear there was a larger story to tell. If the Indian River Lagoon — one of the nation’s most vibrant waterways — could nearly collapse, what did it signal about the rest of Florida?

Sampson teamed with deputy investigative editor Bethany Barnes and investigative data reporter Shreya Vuttaluru to take a deeper look.

They spent more than a year interviewing over 100 scientists, politicians, lawyers and environmentalists about the causes and consequences of water pollution. They analyzed millions of sampling results from a state database to determine whether water quality in the Lagoon and other rivers, lakes and bays showed improvement over the past 25 years.

To observe seagrass beds and manatees up close, reporters traversed Florida — from the Indian River Lagoon to Crystal River — and spent hours on the water.

They submitted more than 140 public records requests to state, regional and federal agencies. Getting information wasn’t always easy. They fought for months and repeatedly had to turn to lawyers to free documents from Florida’s environmental and agricultural agencies.

They reviewed a range of records, from legislative and agency correspondence to manatee necropsy reports. They read more than 7,000 emails from the Florida Fish and Wildlife Conservation Commission written around the time of the starvation die-off. Agency photos provided a rare glimpse into researchers’ response. During the crisis, reporters were not allowed to observe necropsies or accompany scientists in the field.

To understand how environmental regulation shifted in Florida over the past 50 years, reporters combed through thousands of pages at the state archives. These included historic reports on pollution; summaries from past research conferences; and farm trade publications from the 1970s, ‘80s, ‘90s and 2000s.

Ultimately, they found the state failed to control pollutants for decades, allowing the Lagoon and hundreds of Florida waterways to become dangerously polluted. They identified about 1 in 4 waterways tainted by forms of nitrogen, phosphorus or other issues that point to imbalances of the chemicals.

The Florida Department of Environmental Protection said it could not “evaluate or validate” the results of the Times’ analysis, but provided a 20-page response to the reporters’ findings and outlined the state’s efforts to reduce pollution.

The agency said that Florida conducts more water quality monitoring than anywhere in the country.

“When there is more monitoring, it is more likely that water quality issues will be identified,” the department said.

The Times’ work was aided by the Pulitzer Center on Crisis Reporting, which contributed $5,000 to this project through the Florida Climate Reporting Network, which the Times helped create in 2019.

How we analyzed water quality

Our analysis included more than four million sampling points measuring pollution levels in thousands of waterways using data from the Department of Environmental Protection. We examined whether nitrogen, phosphorus and nitrate-nitrite levels were increasing, decreasing or staying the same over 25 years.

Florida is divided into thousands of water segments that vary in size. For instance, the main parts of Tampa Bay are made up of 12 segments, while Lake Tarpon is just one. We considered every individual segment as a waterway and prioritized looking at waters already considered polluted by the Department of Environmental Protection. (For ease and understanding, we also use the word waterway to refer to entire bodies of water, like the Lagoon, that are composed of several water segments.)

We used the Regional Kendall test — a variation of a popular statistical test for identifying environmental trends that accounts for differences in seasonal measurements — to assess the trajectory of water pollution across Florida. The Regional Kendall test was developed by scientists at the U.S. Geological Survey.

Fifteen experts in water quality vetted the statistical analysis and provided guidance on our approach — including technical experts from regional conservation groups, academics and former federal government scientists.

After adjusting for continuity, we had enough data to identify trends in about half of waterways that are considered polluted.

We looked at waterways listed as impaired for nitrogen, phosphorus or nitrate-nitrite and strong indicators of nutrient impairment: algal mats, chlorophyll-a, macrophytes and dissolved oxygen. Waters impaired by these indicators, but not explicitly for nitrogen, phosphorus or nitrate-nitrite, were evaluated for trends in both nitrogen and phosphorus.

There are multiple ways to analyze and interpret trends. The state has performed similar analyses on a smaller subset of monitoring sites. In many places, the Department of Environmental Protection hasn’t stated whether water quality is getting better or worse because it uses a strict interpretation of statistical significance.

Water quality experts and academic texts say such methods can lead regulators to miss important signs about the health of a waterway.

“I believe there's always a trend,” said Robert Hirsch, former associate director of water at the U.S. Geological Survey who reviewed our methods. “You want to know that there’s a non-trivial chance that there is this bad outcome and that you might want to do something about it.”

We instead used a framework that categorized trends based on likelihood, a method recommended by Hirsch that is based on statistical research. In this context, we use the term “likelihood” to refer to an approximate probability that a trend is in the direction reported by the test.

The categories used were “highly likely,” “very likely,” “likely” and “about as likely as not.” Only waters that fell into the “likely” bucket or higher were included when counting trends in our analysis.

Once the trend results were calculated, we sorted them into buckets.

Many water bodies are impaired for multiple nutrients. In these cases, we evaluated each chemical. Because the waterways are already considered polluted, for a segment to be considered improving, all nutrients of impairment had to be clearly decreasing. If levels of one chemical were clearly increasing or maintaining, we considered the segment to be worsening or not getting better overall.

These categories contain a range of results. For example, a “worsening” water may have increasing levels of nitrogen but decreasing levels of phosphorus. Similarly, a water body could have “maintaining” levels of phosphorus and decreasing levels of nitrogen and be labeled as “maintaining” overall. If a water body was impaired for multiple nutrients and decreasing on one but “about as likely as not” to have a trend in either direction on another, we considered that segment to fall in the “ambiguous” category.

Experts differed on whether waters with trends that were “about as likely as not” could fall in the “maintaining” category. We chose to take the more conservative approach. We broke out these cases and assigned them to the “ambiguous” category. This way, we distinguish between water bodies with consistent, high-confidence flat trends and water bodies with scattered measurements that resulted in low confidence of a trend direction.

How we assessed state progress toward pollution reduction goals

We identified 294 water bodies currently listed by the Department of Environmental Protection as having Total Maximum Daily Load targets, or pollution budgets. These waters are identified in the state’s Impaired Waters Rule Database.

Separately, the department publishes a map identifying each water body with a Total Maximum Daily Load. State regulators change water body boundaries and names over time, meaning some of the segments cover different areas and have different IDs today than they did when the targets were first developed. To overcome these discrepancies, we matched the department’s map of water bodies that have Total Maximum Daily Loads to a present-day map of segments and boundaries.

Establishing when each Total Maximum Daily Load was adopted was essential for the analysis. We searched the Florida Administrative Code for these dates and compiled them in a spreadsheet. The year of adoption then became the starting point for running the Regional Kendall test on waterways with targets. The Total Maximum Daily Loads are established in lengthy, scientific reports. We combed through each state report for nutrient-related problems, reading thousands of pages.

Total Maximum Daily Loads are the “heart” of Florida’s approach to reducing pollution in impaired waterways, according to the Department of Environmental Protection. But local governments and business leaders can choose to pursue other avenues, including “alternate restoration plans” and “reasonable assurance plans,” for reducing contamination before state regulators adopt such targets.

We did not analyze the success of these alternate approaches and focused only on Total Maximum Daily Loads as state pollution reduction goals.

How we estimated chemical loads

The Florida Department of Environmental Protection publishes pollution reduction plans for areas around impaired waters. They include modeling results that estimate the amount of nitrogen and phosphorus from land that could enter rivers, lakes and bays.

We examined all of these plans and found that 24 contained comprehensive data to tally an approximate total load across waterways. When the information was available, we also tracked sources the state listed as responsible for the pollution. The pollution sources are identified in broad categories, such as farm or urban fertilizer, and do not identify specific companies or landowners. We entered the figures into a database by hand and summed results for nitrogen and phosphorus.

This allowed us to derive a best-available estimate for how much nitrogen and phosphorus Florida says could threaten impaired waters each year.

There are some caveats. The modeling results are based on land use data from different time periods. Some of the plans haven’t been updated in years. Because Florida has continued to develop rapidly, the estimates may not capture the complete pollution load today. Some of the estimates also may not account for efforts that have been made by the state, local governments and businesses to reduce pollution. The estimates may also include sources beyond runoff, such as discharges from wastewater treatment facilities, atmospheric deposition and loading that the Department of Environmental Protection says is due to natural causes.

Additionally, the Department of Environmental Protection has not included the same information in all of its plans over the last two decades. Some contain detailed breakdowns of pollution totals and sources while others do not.

The sum, ultimately, is likely an undercount of total pollution across Florida. It includes estimates only for land around waterways where the state has implemented restoration plans that involve nitrogen, phosphorus or nitrate-nitrite pollution. That accounts for roughly 38% of the peninsula, according to our analysis.

How we looked at land changes

We relied on a dataset from the U.S. Geological Survey that detects land use changes over time using satellite imagery. The most recent land use classifications were estimated in 2023.

The dataset uses pixels to represent land area. Each pixel is classified based on a type of land use, such as tree-covered land, wetlands or high-density developed land, and covers a 900 square-meter area.

Because the classifications are based on imagery, they may not always reflect exact conditions on the ground. For this analysis, any classifications that were not explicitly listed under “cultivated” or “developed” were considered natural, including designations that could overlap with industrial properties, such as “evergreen forest” used for timberland and “barren land” used as phosphate mines. Some low-intensity housing areas and rural places may be classified as development but contain natural land.

To identify changes across Florida, we calculated the number of pixels that shifted from natural land classifications to any land use classes related to cropland or development between 1985 and 2023. Then, we converted the total pixel area to acres.

How we calculated seagrass losses

We compiled spatial data maintained by Florida water management districts to calculate an estimate of seagrass losses around the state since roughly 2014.

The analysis has some caveats. Seagrass coverage often changes, and surveys only capture specific points in time. Trends in coverage over longer periods may differ from shorter ones. Each region in Florida also measures seagrass on different time scales. For instance, in Estero Bay, surveys were less frequent than in the Indian River Lagoon.

Acreage maps are used by researchers to provide an overview of seagrass extent, but they’re only one indicator of overall health. The thickness of seagrass beds and species type also impact the condition of an ecosystem.

Our loss estimate may be an undercount. We did not include losses in Biscayne Bay, which have been documented in recent years but are not calculated in a measure of area, like square meters or square miles. We also did not include estimates from the Springs Coast, where seagrass cover has reportedly increased by several thousand acres.

Data is more consistent around developed areas such as Tampa Bay and the Lagoon. Some parts of the coast — like areas around Ten Thousand Islands — are not routinely tracked for seagrass acreage and are not included in the surveys. We counted losses in the Big Bend that were derived from a study published in December 2023 by researchers at the Florida Fish and Wildlife Conservation Commission.