Although interest in the use of membranes for the concentration of microalgal biomass has steadily been growing, little is known regarding the phenomena of membrane fouling. In addition, more attention has been given to polymeric membranes compared to ceramic membranes, which have a longer life that is associated with a higher resistance to aggressive chemical cleaning. In this study, microfiltration (MF) and ultrafiltration (UF) of two microalgae species, Chlorella vulgaris and Monoraphidium contortum, were carried out using tubular crossflow ceramic membranes. Permeate flux was measured, resistance was calculated, and dissolved organic carbon (DOC) was determined. The flux reduction during the first 10 min of filtration was higher for MF than UF (>70% and <50%), and steady-state permeate fluxes were <5% (for MF) and <25% (for UF) of initial (in m3 m−2 s−1) 6.2 × 10−4 (for MF) and 1.7 × 10−4 (for UF). Total resistances (in m−1) were in the ranges of 4.2–5.4 × 1012 (UF) and 2.6–3.1 × 1012 (MF) for M. contortum and C. vulgaris, respectively. DOC reduction was higher for UF membrane (>80%) than for MF (<66%) and DOC concentrations (mg C L−1) in permeates following MF and UF were about five and two, respectively. In conclusion, we demonstrated: (i) higher irreversible resistance for UF and reversible resistance for MF; (ii) permeate flux higher for UF and for M. contortum; (iii) the significant role of dissolved organic compounds in the formation of reversible resistance for MF and irreversible resistance for UF.