This paper outlines challenges and opportunities in operating underwater robots (so-called AUVs) on a seaweed farm. The need is driven by an emerging aquaculture industry on the Swedish west coast where large-scale seaweed farms are being developed. In this paper, the operational challenges are described and key technologies in using autonomous systems as a core part of the operation are developed and demonstrated. The paper presents a system and methods for operating an AUV in the seaweed farm, including initial localization of the farm based on a prior estimate and dead-reckoning navigation, and the subsequent scanning of the entire farm. Critical data from sidescan sonars for algorithm development are collected from real environments at a test site in the ocean, and the results are demonstrated in a simulated seaweed farm setup.