The occurrence of the protected species Castor fiber L., which creates a network of natural barriers for its own needs, may affect the changes in water quality parameters. This study shows changes in the water quality parameters (EC, BOD5, COD, TN, N-NH4, N-NO3, N-NO2, TP, P-PO4, Cl−, SO42−) of small rivers in eastern Poland. The results were analysed using the one-way and three-way ANOVA Tukey’s HSD post hoc test to identify the significance of the changes in the water quality parameters for habitats, seasons, and land use. All parameters, with the exception of P-PO4, met the standards of a good ecological status. The average values of P-PO4 exceeded the threshold of the good ecological status in summer and meadows. The average annual changes in the water quality parameters, with the exception of N-NH4, are characterised by a decrease in pollution. The highest concentration decrease of 57% was found for P-PO4 and 45% for TP at the sites after the barriers. The lowest concentration decrease of 5% was found for EC. In the case of N-NH4, the concentration increase was 33%. The situation was completely different in the case of removing barriers, where an increase in the concentration of pollutants of about 30% was found. Changes in the water quality were significantly influenced by the season and land use. Due to the various construction, age, and removal of the barriers, beaver habitats may positively or negatively impact the water quality. It is crucial for the improvement of the water quality to ensure the durability of the functioning of barriers and the proper use of the land.