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Swim-with-whale tourism is a lucrative and rapidly growing industry worldwide. Whale-watching can cause negative effects on the behaviour of targeted animals. Although this is believed to be particularly true for close-up interactions, such as swim-with operations, few empirical studies have investigated this. In 2016, the Western Australian State Government commenced a swim-with humpback whale (Megaptera novaeangliae) trial in the Ningaloo Marine Park, where 11 commercial licences were granted. The swim-with trial was conducted during both the northern and southern whale migration (August to November), during which we assessed potential short-term behavioural effects on humpback whales to swim-with activities. From both an independent research vessel (n = 300 h) and on-board commercial swim-with vessels (n = 357 h), we collected group-follow data (n = 224) on whale behaviour before, during and after swim-with activities. Behavioural effects on whales were investigated, including movement patterns (deviation and directness index, heading, swim speed), surfacing patterns (dive duration and respiration rate) and occurrence of agonistic behaviours. Results showed that the most common type of vessel approach to place swimmers in the water was in the path of whales (89.8% of interactions). During in-path approaches, vessels travelled significantly faster (P = .002) compared to when approaching from the side (side/line abreast approaches). When vessels approached in the whales' path, whales exhibited horizontal and vertical avoidance strategies by adopting a less predictable path (deviating from 32° to 46°), increasing turning angles away from the vessel (heading from 73° to >90°), increasing swim speeds (from 1.68 to 1.89 ms−1), and decreasing the duration of their dives (from 224 to 194 s). Whales displayed a higher frequency of agonistic behaviours when a swim-with vessel was <100 m distance from them compared to >100 m away (P = .011). Young-of-year calves were present during 19.6% (18 of 92) of group-follows that included swim attempts. To reduce potential impacts on whales and increase swimmer safety, we recommend to avoid in-path vessel approaches, not place swimmers in the water with groups of whales that perform agonistic behaviours, and avoid swimming with young-of-year calves