We monitored the succession of nitrifiers in a ne.wly opened wastewater treatment plant for five weeks. After the first distinct decrease in total nitrogen, we began monitoring the appearance, size and number of nitrifying bacteria colonies using the fluorescence in situ hybridization (FISH) method. Ammonia oxidizing bacteria (AOB) colonies were visualized under green excitation as red, and nitrite oxidizing bacteria (NOB) colonies were visualized under blue excitation as green. The changes in protozoan community were monitored simultaneously. Ciliates were divided into four functional groups: predatory, bacterivorous free-swimming, bacterivorous crawling, and sessile. The results showed that at the time of the first distinct total nitrogen decrease, the mean length of both AOB and NOB were relatively low, but the colonies, especially those of nitrite oxidizers, were abundant. In time, the distribution of ammonia oxidizer colonies shifted towards larger sizes, but their quantity decreased. In the case of nitrite oxidizers, a similar trend was noticeable but less pronounced. These changes corresponded with an increasing number of crawling bacterivorous ciliates dominated by the “scavenger” genus Aspidisca. The increasing size of nitrifier colonies may have been due to the growing grazing pressure from crawling bacterivorous ciliates. The strong grazing pressure did not negatively affect N-NH₄⁺ removal effectiveness.