We examine the effect of uncertainty in salmon run abundance and run timing on the ability of managers to achieve escapement goals using in-season regulation of fishery openings using a detailed model of the arrival of salmon and operation of the fishery, the information available to managers, and managers’ behavior. We supplement this management strategy evaluation by examining historical management performance of sockeye salmon (Oncorhynchus nerka) fisheries from Bristol Bay, Alaska. We find that uncertainty about run timing exacerbates the effects of uncertainty about salmon abundance. Early-arriving small runs and late-arriving large runs are especially problematic, as they produce in-season data that mimic that of a typically sized run with average run timing. Managers faced with an early-arriving small run will tend to overharvest the fish, particularly the earliest-arriving component. Managers faced with a late-arriving large run will tend to underharvest the fish, and harvest the latest-arriving components at a higher rate. This differential harvest of early or late components of the run is important because it might reduce the genetic diversity of the stock, thus reducing its future productivity.