The European flounder (Platichthys flesus) is a marine flatfish with high plasticity in several life-history traits, including spawning sites and habitat use patterns. With the overarching goal of understanding the use of estuaries in connection with maturation and reproduction in adult flounder, this study investigates its reproductive cycle in the Douro Estuary (NW Portugal), at the southern edge of its geographical distribution. Adults were caught by monthly trawling from November 2016 to November 2017. Sex ratio and length-weight relationships were determined. The annual reproductive cycle was described using a combination of gonadosomatic (GSI), hepatosomatic (HSI), and general fish condition (Kn) indices, seasonal gonad development staging (macroscopic and histological), and quantification of plasma sexual steroids. Total sex ratio was 1 M:3 F, and females presented negative allometric growth, while males’ growth was isometric. The various indices consistently indicated that the greatest reproductive activity occurred between January and March, peaking in February. However, some females at advanced reproductive stages (late vitellogenesis), high GSI values and steroid hormone (E2) levels were observed as late as May. Females in spawning condition, i.e., undergoing full oocyte maturation and ovulation, were never found, unlike males who exhibited spermiation within the estuary. Sexual differences in migration patterns were also suggested: males seem to leave earlier and stay longer in offshore spawning grounds, while females return to the estuary shortly after spawning. Overall, there was a good correlation between GSI, seasonal hormone cycling, and sexual maturity of female and male flounder, supporting the use of circulating sex steroids as a less invasive tool to assess maturity status.