Over the past few decades, various causal connections between commercial small pelagic fish species and gelatinous zooplankton have been reported in the Black Sea, which affect the pelagic ecosystem. Recently, moon jellyfish regained dominance among gelatinous plankton; however, biomass fluctuations and interactions with small pelagic fish remain poorly understood. During the summers of 2019–2022, scientific pelagic trawl surveys in the Western Black Sea enabled simultaneous monitoring of small pelagic fish biomass, with sprat as the key species and moon jellyfish as an incidental catch. In total, 153 trawl hauls were conducted across four depth strata from 15 to 100 m, and a “swept area” method was used for biomass estimation. The sprat stock biomass ranged from 10,698 to 29,177 t, with an average value of 19,432 ± 4834 t. The total biomass of moon jellyfish was 2002 ± 868.73 t, and dense aggregations were observed in the coastal waters during certain years. Two scenarios of spatial interactions between planktivorous species were identified and linked to the formation of A. aurita aggregations. We found that changes in jellyfish density were associated with weak-to-moderate effects on the spatial distribution of sprat assemblages in coastal areas.