Current estimates of the threatened southern distinct population segment of the North American green sturgeon ( Acipenser medirostris) combine a plot-sampling density estimator with Dual frequency IDentification SONar (DIDSON) and adaptive resolution imaging sonar (ARIS) sonar data. From 2020 to 2022, we annually collected images of all known green sturgeon aggregations and compared the established method to an N-mixture model using side-scan sonar images. We compared 18 different N-mixture model combinations and chose an overdispersed Poisson model that produced estimated abundances of 742, 1286, and 1208 for 2020–2022, respectively. These numbers are ∼2 times greater than the previous method and, if sustained, would fulfill a key criterion for green sturgeon recovery. N-mixture models are known to be sensitive to violations of assumptions, such as the highly dispersed data from our study that caused serious issues, and we recommend practitioners make judicious use of overdispersion and goodness-of-fit tests and be able to identify parameter confounding between detectability and abundance estimates. For our green sturgeon, we recommend simpler population estimates and to focus future energy on reducing variability in the data collection process.