The Te Arawa Rotorua Lakes Programme continues to implement measures to maintain and restore lake water quality in line with trophic level indices (TLI’s) for respective lakes. In Lakes Rotorua and Rotoiti this has also meant not only reducing nutrients to and in the lakes but also managing periodic cyano-bacterial (blue-green) algal blooms. Restoration measures in the Rotorua and Rotoiti catchments have included land use management efforts to arrest nutrient inputs; diversion of Lake Rotorua waters from entering Rotoiti; sewage reticulation of lakeside communities; and treatment of inflows with aluminium sulphate (alum). While restoration efforts have produced water quality gains in both lakes, in recent years, cyano-bacterial blooms have occurred in the shallow embayment of Lake Rotoiti, known as Okawa Bay. These water quality gains have not come without a cost. Submerged aquatic weeds such as Hornwort are an increasing problem in the Rotorua Te Arawa Lakes and significant resources are needed to manage infestations primarily for aesthetic and recreational amenity. Control of exotic aquatic weed is mostly with application of herbicide. Herbicide treatment leaves a decomposing biomass in the waterbody, potentially increasing the nutrient status. We examine the impact aquatic weed decomposition has had on Okawa Bay’s nutrient status and the cyano-bacterial blooms over recent summers, and Bay of Plenty Regional Council’s response to reduce localised bloom development.