The transfer to seawater (SW) represents a critical stage in the production of Atlantic salmon. The success of the transfer links with the optimal development of hypo-osmoregulatory capacities during smoltification. While various strategies are adopted in aquaculture to stimulate smoltification, considerable fish loss still occurs after transfer to sea cages. Therefore, we investigated the molecular responses in the anterior and posterior intestine of Atlantic salmon, following 1) a photoperiod treatment (24 h light (L):0 h dark (D) → 24 L:0D vs. 7 L:17D → 24 L:0D) and 2) dietary treatment (regular feed or feed enriched with a salt mix/tryptophan), combined with, or without a photoperiodic treatment in freshwater (FW), to evaluate how intestinal osmoregulatory mechanisms are modulated by these treatments, and to identify potential intestinal markers indicative of a SW-ready smolt. Using quantitative real-time PCR (qPCR), we investigated transcript levels of transporters and channels involved in ion movements through the enterocytes, tight junction components, and receptors (i.e., calcium-sensing receptor and prolactin receptor). The two intestinal regions showed different gene profiles and responsiveness towards the experimental treatments. In the anterior intestine, the exposure to short photoperiod (7 L:17D) upregulated Na+/K+ − ATPase subunit alpha 1c (nkaα1c), Na+/K+/2Cl− cotransporter 1 (nkcc1), Na+/K+/2Cl− cotransporter 2 (nkcc2), Cl−/HCO3− exchanger Slc26a6 (slc26a6), and cystic fibrosis transmembrane conductance regulator I (cftrI), in FW and SW. Also, Na+/K+ − ATPase subunit alpha 1b (nkaα1b), occludin (ocln), and prolactin receptor (prlr) were upregulated in FW and claudin 15 (cldn15) in SW groups exposed to this photoperiod. The posterior intestine was less responsive to the experimental treatments, although upregulation of nkcc1, nkcc2, slc26a6, and cftrI was observed in FW in the short photoperiod groups. Hence, our findings show that exposure to a winter signal in FW more effectively activates hypo-osmoregulatory mechanisms in the intestine of Atlantic salmon, where a coordinated and complementary role of the anterior and posterior intestine ensures optimal SW processing. Dietary treatment had a positive but more marginal effect on the regulation of the genes investigated, mainly enhancing the impact of short photoperiod when the two treatments were combined. Overall, we propose the apical Na+/K+/2Cl− cotransporter, nkcc2, and the apical Cl−/HCO3− exchanger, slc26a6, as potential FW molecular markers in the anterior intestine to assess “SW-readiness” in Atlantic salmon smolts.