Seasonal effects of rainbow trout (Oncorhynchus mykiss) breeding in traditional, flow-through ponds on abundance and activity of bacteria, and on pools and cycling of dissolved free and combined amino acids (DFAA and DCAA), were studied in three aquaculture systems in Denmark. The fish breeding was found to increase both abundance and production of bacteria by about 60% (annual average of all three systems). The bacterial production correlated positively with temperature, and was 10 to 60-fold higher in summer than winter. Concentrations of DFAA (range: 45–690 nM) increased by 40–350% (mean of 89%) during passage in the systems. The bacterial uptake of DFAA was stimulated by 42% (annual average value of the three systems) between inlets and outlets. Uptake of DFAA was estimated to sustain from 45% (C) and 70% (N) of the bacterial C and N demand. Concentrations of DCAA, e.g., proteins and peptides, varied from 600 to 3900 nM, and increased on average 89% during passage in the three systems. Bacterial capacity for utilization of DCAA was determined as leucine peptidase activity and related to the bacterial density. The cell-specific peptidase activity was, on average, 103% higher at outlets than inlets. Changes in the peptidase activity did not correlate with variations in DCAA pools or the bacterial production. Concentrations of ammonium, urea and phosphate increased on average by 88%, 103% and 66%, respectively, during passage in the three systems, whereas no changes were observed for nitrate. Our study shows that traditional fish breeding impacts pools and cycling of dissolved organic N, as well as bacterial dynamics. The short residence time of water in the ponds (3–6 h) implies that most of the nutrients produced in the systems were discharged into the downstream water, rather than assimilated by bacteria within the systems.