Abstract Cod is usually monitored for scientific purposes using bottom trawl surveys, although its regular pelagic occurrence is well documented. Here we analysed, using Generalized Additive Models, the spatio-temporal changes in the Eastern Baltic cod adult population using pelagic catches from an acoustic survey covering 37 years and the whole central Baltic Sea. Our analysis shows that in the northern areas cod catch per unit effort (CPUE, kg h-1) was high in the early 1980s whereas it dropped and remained very low thereafter. Conversely, in the southernmost area CPUE largely oscillated after the early 1990s. Our model was able to capture key ecological features of the Baltic cod such as preferred depth of occurrence and response to hypoxic conditions. The model also revealed a clear daily cycle of CPUEs, indicating diel vertical migrations at the population level. The temporal trends of pelagic CPUEs generally followed those from the bottom trawl surveys, although differences were observed especially in the recent years with a relative decline in the cod occurring in the pelagic waters. Our results point to the great potential of acoustic survey trawl catches to complement bottom trawl surveys for investigating the spatio-temporal population dynamics and behaviour of the Baltic cod.