1. Disturbance by alien, herbivorous and benthivorous fish species has previously been found to limit the colonization of native charophytes in Lake Rotoroa, Hamilton. This paper compares two methods to reduce the impact of fish on charophyte establishment in this water body. 2. A 1 ha compartment of the lake was partitioned off and intensively fished by conventional netting methods. A total of 5115 fish, total weight 451 kg, was removed from the compartment over 17 months. Allowing for growth and reproduction within the sampling period, intensive netting reduced the original fish biomass by 86% from about 200 to 28 kg ha-1. 3. Catfish (Ameiurus nebulosus Le Sueur) comprised 74% of the fish numbers and 57% of the fish biomass. Perch (Perca fluviatilis L.), shortfinned eel (Anguilla australis Richardson), rudd (Scardinius erythrophthalmus L.), tench (Tinca tinca L.), and goldfish (Carassius auratus L.) were present, in order of reducing abundance. These species are alien to New Zealand, with the exception of shortfinned eel. 4. Charophytes were transplanted inside and outside of the fished 1 ha compartment and their subsequent survival and establishment was monitored. Despite the extensive fish removal from the 1 ha compartment, repeat transplants inside it did not establish in the long term. 5. Outside of the 1 ha compartment, charophytes were also transplanted into nine 6.25-m2 fish exclosures with netting sides to establish founder colonies of charophytes. Within these small exclosures, charophytes established (75% cover) within 1 yr; when five of the exclosures were removed, these unprotected plants survived and expanded over the next year. 6. This study shows that small exclosures can be used to establish founder colonies of charophytes in the presence of herbivorous and benthivorous fish, and that intensive fish removal is likely to be a less successful and more costly method to restore charophytes in lakes.