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Threats derived from marine traffic are diverse, including noise pollution and collisions with air-breathing vertebrates. These specific issues are emerging threats around the Galapagos Archipelago, which is an important site for endangered green turtles (Chelonia mydas). The environmental authorities have committed to promote responsible navigation within the Galapagos Marine Reserve (GMR), prompting this PhD thesis. Chapter 1 provides an overview of vessel strikes and underwater noise pollution, highlighting the relevant policy frameworks. In Chapter 2, we characterised the marine traffic within the GMR using Automatic Identification System data, focusing on four high-use turtle areas. We determined: (i) vessel type, (ii) the number of transits per hour, and iii) vessel speed. Next, we constructed a collision risk model using AIS data combined with in situ information on sea turtle diving behaviour and density. The most effective measures to reduce collisions are either directing vessels away from high-use areas or reducing the number of vessels. However, where this is not possible, a compromise speed limit of 7.5 knots should be introduced to reduce the lethality of vessel strikes. Chapter 3 focusses on vessel traffic and its contribution to underwater noise. We recorded soundscapes over a diel cycle at locations which varied in their level of human activity. Differences were evident between locations and with time of day, corresponding with human activity and vessel type, providing important baselines to assess the extent of noise pollution. Chapter 4 considers the behaviour of free-ranging turtles in the presence of vessel noise. Using state-of-the art-devices, we simultaneously recorded ambient soundscapes and turtle behaviour in situ and found that the duration of travelling and the time spent scanning increased with duration of vessel noise exposure. Finally, Chapter 5 synthesises the salient points from the thesis to inform conservation strategies within the GMR and support sustainable eco-tourism practice.