Management efforts to rehabilitate lake trout Salvelinus namaycush in Lake Superior have been successful and the recent increase in their numbers has led to interest in measuring biomass of pelagic prey fish species important to these predators. Lake Superior cisco Coregonus artedi currently support roe fisheries and determining the sustainability of these fisheries is an important management issue. We conducted acoustic and midwater trawl surveys of the western arm of Lake Superior during three periods: summer (July-August), October, and November 2006 to determine if a single survey can be timed to estimate biomass of both prey fish and spawning cisco. We evaluated our methods by comparing observed trawl catches of small (<250 mm total length) and large fish to expected trawl catches based on acoustic densities in the trawl path. We found the relationship between observed and expected catches approached unity over a wide range of densities, suggesting that our acoustic method provided reasonable estimates of fish density, and that midwater trawling methods were free of species- and size-selectivity issues. Rainbow smelt Osmerus mordax was by number the most common species captured in the nearshore (<80 m bathymetric depth) stratum during all three surveys, while kiyi Coregonus kiyi was predominant offshore except during November. Total biomass estimates of rainbow smelt in the western arm were similar during all three surveys, while total biomass of kiyi was similar between summer and October, but was lower in November. Total biomass of large cisco increased substantially in November, while small bloater Coregonus hoyi biomass was lower. We compared our summer 2006 estimates of total fish biomass to the results of a summer survey in 1997 and obtained similar results. We conclude that the temporal window for obtaining biomass estimates of pelagic prey species in the western arm of Lake Superior is wide (July through October), but estimating spawning cisco abundance is best done with a November survey.