Metal-organic frameworks (MOFs) are attracting increasing interests as photocatalysts for solar-driven hydrogen production from water. This paper reports on a comparative study of using either acetic acid (AA) or trifluoroacetic acid (TFA) as the representative UiO-66 organic modulators for synthesizing visible light responsive UiO-66(Zr)-X (X: NH₂ or NO₂) photocatalysts for water splitting. The results show that photocatalytic hydrogen generation from a water/methanol mixture can be improved by varying the nature and amount of the modulator employed to prepare the different UiO-66(Zr)-X (X: NH₂ or NO₂) solid derivatives. UiO-66(Zr)-NH₂ was the most active photocatalyst, followed by UiO-66(Zr)-NO₂, both prepared with 12 equivalents of AA with respect to the organic ligand. This UiO-66(Zr)-NH₂ solid was more active than the parent MOF in photocatalytic overall water splitting (OWS) (H₂ and O₂ production of 450 and 160 μmol·g⁻¹, respectively, in 5 h; apparent quantum yield (AQY) at 400 nm of 0.06%) in the absence of methanol and compares favourably with analogous reports. Information on the photocatalytic activity of the most active solids of both series was obtained by means of a series of techniques, including ultraviolet–visible (UV−vis) diffuse reflectance, X-ray photoelectron spectroscopy (XPS), laser flash photolysis (LFP), electron spin resonance (ESR), photoluminescence and photoelectrochemical measurements together with density functional theory (DFT) calculations. The results showed that organic acid modulators can be used to enhance the photocatalytic activity of missing linker UiO-66 defective materials in solar-powered water splitting.