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Summary Motile cilia defects impair cerebrospinal fluid (CSF) flow and can cause brain and spine disorders. The development of ciliated cells, their impact on CSF flow, and their function in brain and axial morphogenesis are not fully understood. We have characterized motile ciliated cells within the zebrafish brain ventricles. We show that the ventricles undergo restructuring through development, involving a transition from mono- to multiciliated cells (MCCs) driven by gmnc. MCCs co-exist with monociliated cells and generate directional flow patterns. These ciliated cells have different developmental origins and are genetically heterogenous with respect to expression of the Foxj1 family of ciliary master regulators. Finally, we show that cilia loss from the tela choroida and choroid plexus or global perturbation of multiciliation does not affect overall brain or spine morphogenesis but results in enlarged ventricles. Our findings establish that motile ciliated cells are generated by complementary and sequential transcriptional programs to support ventricular development., Graphical abstract, Highlights • Glutamylated tubulin is enriched in cilia of foxj1-expressing cells in the zebrafish • Motile ciliated ependymal cells in the zebrafish forebrain are highly diverse • Gmnc drives the transition from mono- to multiciliated cells at juvenile stage • Lack of multiciliation does not impact brain and spine morphogenesis, D’Gama et al. dissect the genetic mechanisms underlying the formation of motile ciliated ependymal cell types in the zebrafish forebrain and their function in brain and spine morphogenesis. They show that an increasing diversity of ependymal lineages depends on the sequential or parallel activation of foxj1- and gmnc-dependent transcriptional programs.