The Upper Mississippi River (UMR) represents one invasion front to bigheaded carps Hypopthalmichthys spp. in North America. Agencies often sample larvae to determine the conditions that bigheaded carp reproduction occurs, but the ability for conventional ichthyoplankton sampling to detect bigheaded carp reproduction compared to native fish is unknown. We used occupancy models to estimate larval bigheaded carp and native fish larvae detection probabilities and assessed how habitat type, Julian date, river discharge, and water temperature affect occupancy. We sampled larvae in pools 18-20 of the UMR every two weeks at the Iowa, Skunk, and Des Moines River confluences in backwater, side channel, and thalweg habitats. Detection probabilities increased with water volume filtered and was lower for larval bigheaded carp than freshwater drum, gizzard shad, and percids. Freshwater drum and bigheaded carp larvae had higher detection in thalweg and channel border habitats compared to backwaters. Occupancy of bigheaded carp peaked on June 19 ^th at 20°C, increased with discharge, and declined with coefficient of variation (CV) of water temperature and discharge. Gizzard shad and percids occupancy peaked on May 24 ^th and increased with CV of water temperature while occupancy of freshwater drum peaked on July 3 ^rd, decreased with CV of water temperature, and increased with water temperature. Our results indicate bigheaded carp are more difficult to detect than native larvae and identified conditions associated with larval occupancy that can be used to maximize detection and better understand when, where, and under what conditions larvae are present while accounting for imperfect detection.