Cisco (Coregonus artedi) support an evolving commercial roe fishery in Wisconsin waters of Lake Superior. To monitor trends in spawning cisco abundance, fishery managers recently began estimating adult biomass and exploitation using fall hydroacoustic surveys, which were combined with gill net surveys to inform apportionments of acoustic data. The gill net survey design consisted of paired top-suspended and bottom-set gill nets, but only the sex ratios from top nets are currently used with the hydroacoustic surveys due to an assumption that cisco in Lake Superior are pelagic spawners. However, the vertical sex distribution of cisco during spawning aggregations has been described as dynamic, with males becoming more bottom-oriented throughout the spawning season. We used multilevel aggregated binomial regressions to: 1) determine if there is bias between top and bottom gill net catches of cisco for either sex and if it changes throughout the spawning season, 2) evaluate how the vertical distribution of males and females may create bias in sex ratios used to estimate exploitation, and 3) explore the effect that maturity (i.e., gonadal development) has on vertical distribution during spawning aggregations. We identified sex-specific bias in vertical catch location that has the potential to bias estimates of sex ratio, and the source of this bias may be attributable to maturity driven changes in behavior. These findings highlight a need for caution when relying on gill nets to apportion cisco sex ratios during spawning aggregations and provide support for a non-pelagic alternative hypothesis of spawning behavior.