The lacustrine shrimp Palaemon paucidens undertakes seasonal migration between shallow waters in spring and summer to deep waters in autumn and winter in Lake Biwa in Japan. Previous studies hypothesized that the migration to deep waters was for hibernation. The findings of this study oppose this hypothesis. We showed that P. paucidens is physiologically active in deep waters during winter; that the carbon stable isotope ratio indicated that the species forages in winter and that there was a difference in food sources between summer and winter; that lipid content was highest in January; and that gene expression activity (as measured by the RNA/DNA ratio) remained constant throughout the year. Thus, P. paucidens individuals that migrate to the bottom are likely to forage in winter, but do not hibernate. Nutrients gained in winter were not reflected in individual growth but may have been allocated to gonadal growth and the production of gametes, suggesting that winter foraging by this species in deep sites contributes to obtain resources for reproductive investment. In addition, we found that both small individuals with no reproductive experience and relatively large females with reproductive experience overwintered, indicating that P. paucidens has a life‐cycle that is longer than 1 yr in Lake Biwa.