Two strains of Saccharomyces cerevisiae were tested as probiotics for rainbow trout fry, during the first month of feeding. Each strain was introduced into separate diets, at the rate of 106 CFU g−1 and their effects were compared with those of a control diet. Two rearing conditions were simultaneously compared, to test the adaptability of the probiotic treatment. From start feeding onwards, the water supply came from either spring or river, resulting in two different temperature ranges, 11–11.5 and 7–8 °C respectively. Growth and development were optimal in spring water, while some delay was observed with colder river water. A slight but significant increase in mortality was also observed in the river group. In all groups, the counts of bacteria associated with trout intestine were maximum 10 days post start feeding (dpsf; 107 CFU g−1). The counts of probiotic yeast were also maximum at 10 dpsf (104–105 CFU g−1), but the decrease was slower in river than in spring water. An autochthonous yeast, Debaryomyces hansenii, was also retrieved associated to the intestine of the control group in high numbers after 240 degree days of experiment (104–105 CFU g−1), while the colonization level was significantly less in trout fed the probiotic diets. The effect of the dietary yeast was observed by assaying the activity of three enzymes in the brush border membrane of the enterocytes: alkaline phosphatase (AP), γ-glutamyl-transpeptidase (GGT), and leucine-amino-peptidase N (LAP). At 10 and 20 dpsf, the trout reared in spring water had higher activities of the three enzymes when they were fed the strain S. cerevisiae var. boulardii, suggesting an earlier maturation of the digestive system in this group, compared with trout fed either the other strain of S. cerevisiae or the control diet. The effect was not observed in trout reared in river water with slower growth. Both S. boulardii and D. hansenii seemed to stimulate digestive maturation in fish, but the natural colonization by D. hansenii was likely too late for trout reared at optimal temperature. The supplementation of trout starter diet with S. boulardii may be particularly useful in fast growing conditions.