Cite as: Pauleto, G.M. et al. Intra-annual variation in planktonic ciliate species composition (Protista: Ciliophora) in different strata in a shallow floodplain lake. Acta Limnologica Brasiliensia, 2017, vol. 29, e107. Abstract: Aim: We aimed to evaluate the variation in planktonic ciliate species composition in different strata of the Guaraná Lake, encompassing high and low water periods, at the Upper Paraná River floodplain. Methods: Samplings were collected monthly between March 2007 and February 2008, from the epilimnion, metalimnion and hypolimnion. Ciliates samples were filtered using a plankton net of 10µm mesh size and identified in vivo under an optical microscope. Results: Among 112 species identified, 13 were found exclusively during the high water periods and 39 during the low water period. Results of nonparametric extrapolation indices evidenced that the observed richness represented between 70% and 90% of the estimated richness. Regarding the variation in species composition, Beta1 index showed that the alteration in composition between strata during the low water period was slightly greater than that registered during high waters. Cluster analysis evidenced a higher dissimilarity in ciliate species composition between periods than among the different strata. The greatest variation in species composition was verified during the distinct hydrological periods, whereas no significant differences were observed for the different strata analysed. Conclusions: We found that in the pelagic compartment, ciliate species composition changed significantly between hydrological periods, and a higher similarity in species composition among strata was observed during the high water period. Therefore, alterations in the vertical distribution seem to be related to the homogenizing effect of the floods in the water column stability.Keywords: protist; plankton; species richness; diversity; freshwater.Resumo: Objetivo: Avaliou-se a variação na composição de espécies de ciliados, em diferentes estratos na lagoa do Guaraná, englobando períodos de águas altas e baixas, na planície de inundação do alto Rio Paraná. Métodos: As amostragens foram realizadas mensalmente entre março de 2007 e fevereiro de 2008, em três diferentes profundidades: epilimínio, metalimínio e hipolimínio. Depois de concentradas as amostras em rede de plâncton (10µm), os organismos foram identificados in vivo 2 Pauleto, G.M. et al.