Brown trout is a common type of fish grown for consumption in open and flowing fish ponds on the rivers of Bosnia and Herzegovina. We conducted this study during three seasons (spring, summer and autumn) to obtain a complete picture of the morphological and histological characteristics of selected trout tissues. The physicochemical characteristics of the water from the Pliva River near Pljeva and the fish pond where intensive breeding of trout is carried out were analyzed. These analyses have shown that there are no major deviations in water quality and that the water in the pond is of excellent quality. A total of 90 trout were harvested during all three seasons and their morphometric characteristics were determined by analyzing ten parameters. After the dissection of all individuals, histological and stereological analysis was performed to compare the tissues of the liver, stomach, gills and muscles. These analyses showed significant differences in the histoarchitecture of selected trout tissues from the pond compared to the river. Liver tissue had altered hepatocyte shape and presence of adipocytes; stomach tissue had stronger mucosa and weaker muscle layer; gill tissue had lower respiratory lamellae; while muscle tissue had a significant presence of adipose tissue in brown trout living in the fish pond compared to those in the river. All these changes are due to the quality of commercial feed and the inability to move freely.