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Application of Over 30 Years of FIM Data to Address Myriad Issues

The Fisheries Independent Monitoring (FIM) program at FWRI strives to provide timely, fisheries-independent data and analysis to fisheries managers for the conservation and protection of Florida’s fisheries. The FIM sampling program was designed to track annual trends in abundance, as well as changes in size and age composition over time. The program supports single-species assessment and management, multi-species and ecosystem-based modeling and management, as well as emerging issues. Because the FIM program uses a multi-gear approach (many different types and sizes of capture gear) to collect information on a suite of species and size/age classes, FIM data have many applications.

The FIM program was established in Tampa Bay and Charlotte Harbor in 1989, based on perceived reductions in red drum (Sciaenops ocellatus) stocks. It was recognized that long-term monitoring should be initiated to track abundance trends of multiple species, not just red drum. Over the years, the FIM program has expanded to other estuaries, and expanded sampling to include a suite of species and life stages. The FIM program has also designed and tested numerous potential sampling gears to maximize the use of the data collected and sampling efficiency. Based on these tests, the program has selected a core suite of gears to implement in long-term monitoring surveys, although other gears are used for smaller, focused studies. When sampling in estuarine waters, FIM biologists generally use three main gear types: a 21.3-m seine, a 183-m haul seine, and a 6.1-m otter trawl. In offshore waters, FIM biologists use side scan sonar to map the ocean floor to determine different offshore habitats and then use cameras, hooked gears, and large trawls to identify, count, and measure fish.

Two images of large nets deployed in the water. A third image of a camera housed in a large metal cage.

Left: An example of one of FIM’s inshore sampling gear types: 21.3-m seine. These nets are set either along shorelines or in shallow estuarine waters and mainly collect small-bodied fishes and juveniles. Middle: An example of one of FIM’s inshore sampling gear types: 183-m haul seine. These nets are set along shorelines and mainly collect larger-bodied fishes. Right: An example of an underwater stereo camera pod used by FIM to count and measure fishes in offshore waters.

FIM conducts research surveys in waters ranging from the tidally influenced portion of rivers to offshore habitats. In nearshore waters, the FIM program has continuous long-term monitoring data in 7 of Florida’s estuaries (Apalachicola, Cedar Key, Tampa Bay, Charlotte Harbor, Jacksonville/St. John’s River area, Northern Indian River Lagoon, and Tequesta/Southern Indian River Lagoon). Recently, FIM has expanded further west in the Florida panhandle to help address management needs for new state management zones. Depending on grant funding, the program will expand into various other estuaries throughout the state. FIM currently has grant-funded monitoring in Sarasota Bay, the western Everglades, and Florida Bay. In offshore waters, the FIM program has grant-funded sampling off both the Gulf and Atlantic coasts.

FIM data collections are standardized throughout the program and statewide, and sampling protocols are maintained through the years. Consistency in these long-term datasets make them an integral part of both state and federal stock assessments for fisheries management. Additionally, routine monitoring allows researchers to assess potential effects on fish populations due to disturbance events like extreme cold events or prolonged red tide and other harmful algal blooms. Having data before, during, and after the event allows the FIM data to better inform management actions.

There are almost 90 staff in the program who help sample thousands of locations every month, rain or shine. FIM’s offshore sampling work is part of larger, collaborative Gulf-wide efforts (G-FISHER reef fish survey, SEAMAP groundfish survey), so federal and state partners assist in collecting data from those areas outside Florida. With a focus on consistent data collection over the years, both inshore and offshore, the FIM program requires carefully documented procedures, extensive training, and periodic cross-training among labs and staff to ensure that standard protocols are being followed. FIM strives for multi-year surveys to track abundance estimates over the years, and also takes biological samples from a subset of the catches to inform biological metrics (age, growth, mercury content, etc.). In addition to routine sampling for population abundance, FIM also has one of the only diet labs in the Gulf of Mexico to analyze the stomach contents of various species. FIM also has a mercury lab to analyze the mercury content in fish tissues. These data are instrumental for ecosystem modeling efforts.

Image on the left is of a smaller white boat with two people onboard traveling in an area near shore. Right image is of a larger vessel travelling in offshore waters.

Left: FIM staff use a mullet skiff to sample inshore, estuarine waters. Notice that the motor is placed in the center of the vessel to shift weight towards the bow to allow sampling in very shallow waters and to give space at the stern for a large net well to deploy nets. Right: FIM staff use various larger vessels to conduct multi-day research cruises to sample offshore waters in the Gulf of Mexico. The one pictured here is the R/V Gulf Mariner, and it is mainly used to deploy cameras for monitoring offshore reef fishes.

FIM is partnered with FWRI’s Fish Bio’s Age & Growth lab to age the fish collected during sampling; the Fish Health program for routine health monitoring as well as special projects; the Harmful Algal Bloom program to supply samples for regular monitoring as well as bloom-specific research; the stock assessment program for assistance in analyzing/synthesizing data for stock assessments; the HSC for some of the grant-funded monitoring work that aids in informing restoration actions. The FIM data are also used by various other research groups in FWRI for population abundance updates, analyses, and publications, since FIM has long-term monitoring data for a suite of fish and invertebrates.

The core work of the FIM program is funded primarily from State of Florida saltwater license sales and funding from the Sportfish Restoration Program. The core work is supplemented by other grants from local, state, and federal agencies to enhance the long-term monitoring surveys or conduct more focused studies. Some years, supplemental funding can comprise up to 50% of FIM’s operating budget.

Ultimately, FIM is a collaborative program. FWRI researchers and biologists actively partner with scientists and funders from dozens of agencies and institutions to work together to monitor fish populations that are important to Florida and address management needs at multiple scales. After all, fish and other wildlife don’t know what a state border is, so managers and researchers need to work across state lines to gain a more complete picture of a species’ life history and population trends. Data or specimens collected by the FIM program have been used in various FWRI projects, graduate student theses or dissertations, and to date, FIM staff have been involved with over 400 scientific publications.


Three people stand around a white container filled with water, dozens of little fish, and one large fish.

Sample workup for FIM includes identifying fish and selected macroinvertebrates to the lowest possible taxonomic unit, counting the individuals, measuring a subset, and releasing most specimens alive. A small subset of specimens is retained for further biological sampling (e.g., otoliths for fish ages, muscle/tissue samples for mercury content). The FIM program collaborates with many groups, universities, and other institutions so we also assist with sample provision for collaborators.

  • The FIM program regularly provides data, especially indices of abundance and size or age composition of fish, for state and federal fisheries managers.
  • Long-term data can be used to assess changes in abundance after disturbances, like potential impacts of red tide.
  • FIM data were also used to assess the response of the Common Snook population to the 2010 cold event, and informed management actions
  • Over the years, the FIM group has been asked to participate in a series of studies on freshwater flow. Some of these studies have informed Minimum Flows and Levels for various rivers in Florida. Recently, the FIM group has secured a 5-year grant to sample in the western Everglades and Florida Bay to assess how estuarine fish abundances may change as a result of some of the water management infrastructure changes that have been made in the Everglades to try to restore historic water flows.
  • After documenting that Common Snook assessments may be better informed with a more powerful young-of-the-year abundance index, the FIM program expanded sampling efforts for juvenile snook in 2016 to produce more powerful indices of abundance for state stock assessments.
  • FIM monitoring data have been used to document expanding species distributions (e.g., Common Snook moving northward into Cedar Key; Lionfish expanding on natural and artificial reef habitats in the eastern Gulf of Mexico and their subsequent decline in recent years).
  • Historically, there was a very limited understanding of the distribution and quality of natural and artificial reef habitat in the eastern Gulf of Mexico at scales that would be useful to determine sites to sample. To meet this need, the FIM program initiated a random habitat mapping survey, using side scan sonar, to identify and classify natural and artificial reef habitats. Because these surveys occur at randomly selected locations, they provide representative estimates of habitat quality and distribution. At over 8,000 km2 mapped, this is the largest mapping effort conducted to date on shelf habitats in the Gulf of Mexico. The FIM habitat mapping survey also periodically revisits sites that were previously mapped, which can provide some information on how habitats change through time, especially in response to large environmental events such as hurricanes.
  • The 2020 regional management plan for Spotted Seatrout created five management regions. The long-term FIM program has a presence in four of the five regions, so data were already being collected that could help inform future management decisions. However, data within the newly established western Panhandle management region were very limited. Due in part to well-established protocols and procedures, along with multiple decades of experience from other systems, the FIM program was able to adapt rapidly. A scaled back version of FIM sampling was established in St. Andrew and Choctawhatchee Bays in 2021 to provide data for Spotted Seatrout and other species. This seasonal program provides data on both juveniles and adults.
  • Data from the Southeast Reef Fish Survey using chevron traps and trap-mounted cameras are the primary fishery-independent data source used for assessing reef fish, including Red Snapper. In a prior Red Snapper assessment, the generally low number of larger Red Snapper in the chevron trap survey was interpreted as indicating that few large, old Red Snapper were present in the population. The FIM program conducted a study to compare the size of Red Snapper caught in traps versus those observed on stereo-video. Results indicated that larger Red Snapper were observed much more commonly on video. These results changed how chevron trap data were incorporated into the assessment model and contributed to the decision to allow very limited Red Snapper harvest in recent years. This is just one example of the many small-scale, focused studies that FIM conducts.