Abstract Aim Knowledge of hydrological characteristics is essential for understanding ecological processes in floodplains, which can support sustainable management. We evaluated environmental variations in a shallow floodplain lagoon located in the Chapada Diamantina, Andaraí, Bahia. We aim to identify phases of the hydrologic cycle and their influence on desmid density, which is a group of algae known for its potential as bioindicator of trophic changes. Methods Bimonthly samplings were performed at four points in the lagoon. Abiotic (temperature, conductivity, pH, transparency, depth, dissolved oxygen, total and dissolved nutrients) and biotic (macrophyte cover, phytoplankton chlorophyll-a, and desmid density) variables were determined. The Trophic State Index (TSI) was calculated based on phytoplankton chlorophyll-a, and total phosphorus concentration. Results The lagoon was characterized by well-oxygenated, slightly acidic waters with low electrical conductivity. According to the TSI, the lagoon varied from mesotrophic to hypereutrophic during the study period. The driest months (August and October) were marked by high water transparency, low depth, nitrogen concentration, and macrophyte coverage. The highest value of accumulated precipitation was registered in December, when there was an increase in depth and a decrease in electrical conductivity and PT concentration. Two phases of the hydrologic cycle were evidenced and determined by the depth and nutrient concentrations. The highest abundance of desmids occurred at the end of the rainy season when the nutrient availability and pH were higher, and the depth was reduced. Conclusions Our results suggest that the flood pulse was the determining factor of the local environmental conditions and that, together with the macrophyte morphological traits, it influenced desmid abundance and distribution in a floodplain lagoon in the semiarid region.