Because fish that enter the interior Delta have poorer survival than those emigrating via the Sacramento River, understanding the mechanisms that drive entrainment rates at side channel junctions is critically important for the management of imperiled juvenile salmon. Here, we implement a previously proposed process-based conceptual model to study entrainment rates based on three linked elements: the entrainment zone, critical streakline, and cross-sectional distribution of fish. The critical streakline is the location along a channel cross-section immediately upstream of a junction that forms the spatial divide between parcels of water that enter a side channel or remain in the main channel. The critical streakline therefore divides the main channel into entrainment zones within which fish would likely enter each channel. Combined with information about the cross-sectional distribution of fish upstream of a junction, this conceptual model provides a means to predict fish entrainment into each channel. To apply this conceptual model, we combined statistical models of the critical streakline, the cross-sectional distribution of acoustic tagged juvenile Chinook salmon, and their probability of entrainment into Georgiana Slough. We fit joint beta regression and logistic regression models to acoustic telemetry data gathered in 2011 and 2012 to estimate the cross-sectional distribution of fish upstream of the junction, and to estimate the probability of entrainment for fish on either side of the critical streakline. We show that entrainment rates can be predicted by understanding how the combination of critical streakline position and cross-sectional distribution of fish co-vary as a function of environmental covariates. By integrating over individual positions and entrainment fates to arrive at population-level entrain probability in relation to environmental covariates, our model offers managers a simple but powerful tool to evaluate how alternative actions affect migrating fish.