Highly stratified marine ecosystems with dynamic features such as fronts or clines in salinity, temperature, or oxygen concentration challenge an individual’s ability to select suitable living conditions. Ultimately, environmental heterogeneity organizes the spatial distributions of populations and hence the spatial structure of the ecosystem. Our aim here is to present a method to resolve small-scale distribution on an individual level, as needed for the behaviorally-based prediction of habitat choice and limits. We focused on the small-scale vertical distribution of cod Gadus morhua L. in the Bornholm Basin, central Baltic Sea, during spawning time in 2 years with different vertical thermohaline and oxygen stratifications. Individual cod were identified by echotracking of real-time in situ hydroacoustic distribution data. In order to resolve and identify hydrographic preferences and limits, ambient parameters including temperature, salinity, and oxygen concentration as well as expected egg-survival probability were individually allocated to each fish. The vertical distribution of hydroacoustically identified fish was compared to data simultaneously recorded by data storage tags attached to cod. The results showed a clear influence of ambient salinity and oxygen concentration on the distribution pattern and distributional limitation of cod during spawning time, and also consistency of data storage tag-derived distribution patterns with those based on individual echotracking. We therefore consider this method to be a useful tool to analyze individual behavior and its implications for the population’s spatial distribution in stratified environments.