Counting towers provide an accurate, low-cost, low-maintenance, low-technology, and easily mobilized escapement estimation program compared to other methods (e.g., weirs, hydroacoustics, mark-recapture, and aerial surveys) (Thompson 1962; Siebel 1967; Cousens et al. 1982; Symons and Waldichuk 1984; Anderson 2000; Alaska Department of Fish and Game 2003). Counting tower data has been found to be consistent with that of digital video counts (Edwards 2005). Counting towers do not interfere with natural fish migration patterns, nor are fish handled or stressed; however, their use is generally limited to clear rivers that meet specific site selection criteria. The data provided by counting tower sampling allow fishery managers to determine reproductive population size, estimate total return (escapement + catch) and its uncertainty, evaluate population productivity and trends, set harvest rates, determine spawning escapement goals, and forecast future returns (Alaska Department of Fish and Game 1974-2000 and 1975-2004). The number of spawning fish is determined by subtracting subsistence, sport-caught fish, and prespawn mortality from the total estimated escapement. The methods outlined in this protocol for tower counts can be used to provide reasonable estimates ( plus or minus 6%-10%) of reproductive salmon population size and run timing in clear rivers.