We suggest helminthological investigations of cod as a supplement to traditional biological and hydrographical methods for elucidation of ecological changes in the Baltic Sea. It is under discussion if oxygen deficit or seal abundance should explain the present critical situation of Baltic cod. A comparative investigation of endoparasitic helminths in Baltic cod (Gadus morhua), captured in the same marine habitat with an interval of 35 years (1983/2018) recorded 11 species of helminths comprising trematodes (Hemiurus luehei, Podocotyle atomon, Lepidapedon elongatum), nematodes (Contracaecum osculatum, Hysterothylacium aduncum, Capillaria gracilis, Cucullanus cirratus), cestodes (Bothriocephalus sp.) and acanthocephalans (Echinorhynchus gadi, Pomphorhynchus laevis, Corynosoma semerme). Significant prevalence and intensity increases were recorded for third-stage larvae of the nematode C. osculatum (liver location) and larvae of C. semerme (encapsulated in viscera). Both parasite species use grey seal as their final host, indicating the recent expansion of the Baltic seal population. A lower E. gadi intensity and an increased prevalence of L. elongatum of small cod (31–40 cm body length) suggest a lowered intake of amphipods (intermediate host) and elevated ingestion of polychaetes, respectively, but no significant changes were seen for other helminths.