Scientists use statistically valid sampling to collect fisheries-independent data to supplement fisheries-dependent information obtained from anglers and commercial fishing operations. These monitoring efforts differ from one another. Fisheries-independent monitoring is a system-wide approach and evaluates numerous species along with their habitat conditions. Fisheries-dependent monitoring, on the other hand, monitors the harvest of individual species as they are taken through commercial and recreational fishing.
Regions are divided into hydrological zones, then stratified (or assigned) into areas by habitat type (i.e.; seagrass, mangrove, depth, shore type, etc.). Monthly sampling is then conducted at sites randomly selected from the strata in each zone to monitor juvenile and adult stocks.
A variety of fishing gear and techniques ensure sampling of fisheries in a wide range of sizes and ages. Smaller seines and otter trawls are used to capture smaller fishes, while larger sub-adults and adult fishes are collected using 183-meter haul and purse seines. The State also employs visual surveys, using divers, for data collection in the Florida Keys Marine Sanctuary.
Data collected includes species, size, sex, and number of individuals per species caught. As part of these monitoring efforts, fish are examined for external lesions or abnormalities, and tissue samples are taken from selected fishes for analysis of mercury content. Biologists also record habitat features such as the type and quantity of submerged and shoreline vegetation and the presence of seawalls or oyster beds. Water quality data (including temperature, pH, salinity and dissolved oxygen) are also collected.