Aquaculture has been a growth industry in Tasmania for the past decade, with Atlantic salmon now the largest aquaculture industry within Australia. With sustained growth of the salmon industry there exists a greater potential for broadscale environmental impact, namely interactions with habitats such as reef and seagrass. More recently, seaweed aquaculture has begun to develop in Tasmania, with a need to better understand natural populations of seaweed for sustainability of this new industry. Over the past eight years we have developed a range of methods for detecting impact from aquaculture on reef and seagrass, including visual assessment through in-situ diver surveys, image capture using remote observational platforms and biochemical sampling. Initially, these techniques were aimed at better quantifying functional change that may occur on reefs as the result of nutrient enrichment from salmon aquaculture, such as the presence of opportunistic or nuisance algae or changes to abundance and composition of the canopy. More recently, these tools have been modified or adopted to support the development of a seaweed industry, where broadscale or baseline assessments of natural populations is important. Each of these methods has their advantages and limitations, with appropriate methods largely dependent on the rationale behind the monitoring program.