Planktonic ciliates occasionally form brief rapid increases in numbers (blooms) that can be trophically important. Although model simulations and mesocosm studies indicate that blooms occur over 10 to 20 days, field data are rarely suffi ciently detailed to reveal their occurrence and demise. Our data (collected over 57 weeks across a coastal lagoon) offer insights into the population dynamics of a single species, place these in the context of the entire ciliate assemblage, and provide guidance on what should continue to be examined. Specifically, to evaluate population dynamics we examine two species of Cyrtostrombidium, characterise temporal and spatial variation of their abundance, and relate these to abiotic phenomena and biological factors. This is also the first report of Cyrtostrombidium in a tropical coastal lagoon. Collectively our analysis reveals key aspects of the dynamics of this genus: 1) small-scale peaks in abundance are ~30 m in size and can persist for ~10–30 days, reaching a maximum of 100 cells ml–1; 2) these increases are driven by biotic factors (revealed through autocorrelation analysis); 3) long-term trends are driven by the shift between dry and rainy seasons and by the periods of isolation of lagoon from the sea (revealed through multiple regression analysis); 4) blooms may at times control primary production; 5) conjugation, an ecologically important event, may be associated with blooms (at times 9% of population was conjugating); and 6) dinoflagellate parasitism, poorly described in oligotrichs, is potentially important in population demise. These results both reflect on how ciliates may behave in short-term events and should encourage the continued need for detailed observations of field samples at a high taxonomic resolution.