Abstract: Intermittently closed and open lakes and lagoons (ICOLLs) are shallow barrier lakes which are intermittently connected to the sea and experience saline intrusions. Many ICOLLs are mechanically opened to prevent flooding of surrounding agricultural and urban land and to flush water of poor quality. In this study, the effects of modified opening regimes (frequency and duration of barrier openings and closures) on water quality and phytoplankton in two New Zealand ICOLLs were investigated over a number of opening/closure cycles. Water quality in Lake Ellesmere (Te Waihora) responded weakly to both opening and closing events, indicating that sea–ICOLL exchange did not markedly improve water quality. Conversely, water quality in Waituna Lagoon responded rapidly to barrier openings; water level decreased to near sea level within days of opening and subsequent seawater exchange resulted in rapid decreases in nitrate and chlorophyll a concentrations. The closure of Waituna Lagoon resulted in rapid rise in water level and a pulse of nitrate and phosphorus in the water column and phytoplankton chlorophyll a concentrations increased with increasing closed-period duration. Based on data on the underwater light climate and nutrient dynamics, phytoplankton in Lake Ellesmere was probably light-limited, whereas phytoplankton in Waituna Lagoon was rarely light-limited, and appeared to be predominately P-limited. The marked differences in responses of Lake Ellesmere and Waituna Lagoon to barrier openings and closures reflected differences in ICOLL water levels and morphological characteristics, which dictated the degree of tidal flushing when the barriers were open. The inter-ICOLL differences observed in this study indicate that unless the effects of ICOLL openings/closures on phytoplankton and nutrient dynamics are understood, changes to ICOLL opening regimes may have unintended consequences for the water quality and ecology of these systems. [Copyright &y& Elsevier]