The Atlantic salmon shows substantial life cycle plasticity, which also applies to the timing of puberty. While it is characterized by the activation of the brain–pituitary–gonad axis, many morphophysiological aspects of puberty and the influence of environmental conditions, such as water salinity, are not well understood in fish. Here, 12-month-old Atlantic salmon coming from an out-of-season smoltification regime in December were exposed to freshwater (FW) or seawater (SW) at 16 °C to stimulate puberty under a 24-h constant light (LL) or 12 h light:12 h darkness (LD) photoperiod. These four treatment groups (FWLL, SWLL, FWLD, and SWLD) were studied from January to March. Next to 11-ketotestosterone (11-KT) plasma levels, the expression of pituitary genes (gnrhr4, fshb, and lhb) and spermatogenesis was quantified. When spermatogonial proliferation started, fshb mRNA levels increased steeply and began to decrease when spermatogonial mitosis approached completion and most germ cells had reached meiotic or post-meiotic stages. Conversely, lhb mRNA levels increased progressively during spermatogenesis. Most males in all treatment groups matured, but exposure to SW resulted in the strongest stimulation of the onset of spermatogenesis and elevation of pituitary gnrhr4 and fshb mRNA levels. Later on, the LD photoperiod accelerated, irrespective of the salinity, the completion of spermatogenesis, associated with higher lhb mRNA and 11-KT plasma levels than in the LL groups. We find that both salinity and photoperiod modulated different aspects of spermatogenesis, and resulted in a differential activation of pituitary and testis functions; SW stimulating the onset and the shorter photoperiod the completion of spermatogenesis.