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Fish are the most widely used organisms in NAWQA tissue analysis programs. The appeal for the use of fish in biomonitoring lies in their economic importance, their large size, and their position at the top of the trophic scheme of aquatic systems. The are also the primary source of food for important animals such as fish-eating birds, and they provide a direct pathway for human exposure to contaminants.

Two methods are used in the collection of fish for tissue analysis. The primary collection method is electrofishing, while seining is a secondary technique.

Electrofishing
Electrofishing is the use of electricity to capture fish. Towed electrofishing gear is used for sampling fish in wadeable streams. The power source is either a 24-volt deep cycle battery or a 115-volt gasoline-powered generator. Electrical current stuns the fish and draws them toward the anode, the positive end of the current.

Towed electrofishing, where a portable generator is placed in a boat and towed behind an operator, is done in streams greater than 1 meter deep and 5 meters wide. Electrofishing crews requires three to six individuals, with members either operating the electrofishing equipment, collecting fish with dip nets, or transferring fish to the holding container. Sampling begins at the downstream boundary of the sampling reach and is conducted in an upstream direction. This maximizes visability and collection efficiency.

Nonwadeable streams are sampled using electrofishing boats. These boats are usually made of aluminum and have a gasoline-powered generator and an electrical output control mechanism.

Seining
Seining is a method for collecting small fish and complements electrofishing to obtain a representative sample. Seines are collection devices that trap fish by enclosing or encircling them. Seines consist of a mesh panel with weights on the bottom, floats at the top, and poles on each side. The smallest seine is known as a "common sense" seine whereas a seine 7.6 or 9.1 meters is known as a "bag" seine. A "bag" seine is so named because it has a bag or packet in the center. Seining is usually done downstream where it is the most effective in collecting fish.

For the LIRB, seining was mostly conducted in wadeable streams. In wadeable streams, relatively free from obstructions, the bag seine is used. In riffle areas, a common sense seine is used with a technique known as "kick seining." Two people hold the seine above the water, perpendicular to the flow. Then the poles and lead line of the seine are thrust to the stream bottom. A slight pocket in formed in the seine as the poles are allowed to slant downstream. A person, upstream of the seine, kicks the substrate working downstream toward the seine. The channel is crossed and the seine is lifted out of the water and the fish removed.

Each sample consists of a composite of whole fish or livers from adult individuals of the same species, all approximately the same size. Composite samples from five or more fish are acceptable, but samples composed of at least eight fish are desired. The confidence in the estimate of the mean concentration of contaminant in the tissue increases as the number of individual samples in the composite increases.