An investigation into the effect of different lengths of intermittent light/dark periods on the photolytic and photocatalytic disinfection of Escherichia coli was undertaken at laboratory scale. Water containing E. coli was pumped around a laboratory scale compound parabolic collector and exposed to UV light in the presence and absence of titanium dioxide photocatalyst. By darkening sections of the reactor tubing, the illumination time and frequency were varied. The disinfection kinetics were studied, as well as the effective disinfection time received for each configuration. For photolysis, it was seen that the number of dark and light periods had very little effect on disinfection, once the illuminated area was kept constant, although having fewer light/dark interfaces was slightly favorable. It was also seen that an increase in the illuminated area reduced the efficiency of disinfection in relation to cumulative UV dose. In photocatalytic tests, it was found that increasing the frequency of light/dark periods, while keeping the illuminated area constant, had a beneficial effect on disinfection, both in terms of time to method detection limit (MDL) and effective disinfection time (EDT). In post irradiation tests, where samples were kept in the dark for 48 h after illumination, photocatalysis was seen to have a distinct advantage over photolysis, with total inactivation achieved within 60 min for all configurations, as opposed to a minimum of 180 min in photolytic tests. From an engineering design perspective, the above findings could lead to smaller, more efficient reactor configurations. The implications that more interruptions improve photocatalytic disinfection could be implemented by introducing light and dark periods into photocatalytic reactor systems, subject to further testing.