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Abstract Gelatinous zooplankton serve diverse ecological roles in shelf food webs—from grazers to predators. However, their spatial niches are poorly resolved, especially at detailed taxonomic levels, due to conventional techniques that are unable to measure distributions at fine spatial scales. Seasonal in situ imaging transects across the dynamic northern Gulf of Mexico demonstrated that taxonomic diversity of gelatinous zooplankton increases with stratification and habitat heterogeneity. Taxa displayed low spatial niche overlap (~ 10%, Schoener'sD), independent of season (stratified, river‐influenced, and well mixed), and even when associated with similar water mass properties. This suggests that oceanography structures the distributions of gelatinous organisms and water mass preferences, but ecological interactions among taxa generate distinct taxon‐specific spatial niches. Although automated image classification algorithms currently prioritize broad taxonomic groups, detailed identifications and improved resolution of interactions (predator–prey, competition, etc.) may underlie a predictive framework for gelatinous abundances and diversity.